ROI

java.lang.Object
- icy.roi.ROI

All Implemented Interfaces:

ChangeListener, XMLPersistent

Direct Known Subclasses:

ROI2D, ROI3D, ROI4D, ROI5D
```
public abstract class ROI
extends java.lang.Object
implements ChangeListener, XMLPersistent
```

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`ROI.ROIGroupId` Group if for ROI (used to do group type operation)
`static class`	`ROI.ROIIdComparator`
`static class`	`ROI.ROINameComparator`
`class`	`ROI.ROIPainter` Abstract basic class for ROI overlay

Field Summary

Fields
Modifier and Type	Field and Description
`static java.awt.Color`	`DEFAULT_COLOR`
`static java.awt.Color`	`DEFAULT_NORMAL_COLOR` Deprecated. Use `DEFAULT_COLOR` instead.
`static float`	`DEFAULT_OPACITY`
`static double`	`DEFAULT_STROKE`
`static java.awt.Color`	`defaultColor`
`static java.lang.Float`	`defaultOpacity`
`static java.lang.Boolean`	`defaultShowName`
`static java.lang.Double`	`defaultStroke`
`static java.lang.String`	`ID_CLASSNAME`
`static java.lang.String`	`ID_COLOR`
`static java.lang.String`	`ID_GROUPID`
`static java.lang.String`	`ID_ID`
`static java.lang.String`	`ID_NAME`
`static java.lang.String`	`ID_OPACITY`
`static java.lang.String`	`ID_PROPERTIES`
`static java.lang.String`	`ID_READONLY`
`static java.lang.String`	`ID_ROI`
`static java.lang.String`	`ID_SELECTED`
`static java.lang.String`	`ID_SHOWNAME`
`static java.lang.String`	`ID_STROKE`
`static ROI.ROIIdComparator`	`idComparator`
`static ROI.ROINameComparator`	`nameComparator`
`static java.lang.String`	`PROPERTY_COLOR`
`static java.lang.String`	`PROPERTY_CREATING`
`static java.lang.String`	`PROPERTY_GROUPID`
`static java.lang.String`	`PROPERTY_ICON`
`static java.lang.String`	`PROPERTY_NAME`
`static java.lang.String`	`PROPERTY_OPACITY`
`static java.lang.String`	`PROPERTY_READONLY`
`static java.lang.String`	`PROPERTY_SHOWNAME`
`static java.lang.String`	`PROPERTY_STROKE`
`static java.lang.String`	`ROI_CHANGED_ALL`
`static java.lang.String`	`ROI_CHANGED_POSITION`

Constructor Summary

Constructors
Constructor and Description

ROI()

Constructors
Constructor and Description
`ROI()`

Method Summary

Methods
Modifier and Type	Method and Description
`ROI`	`add(ROI roi, boolean allowCreate)` Adds content of specified `ROI` into this `ROI`.
`void`	`addListener(ROIListener listener)` Add a listener
`void`	`attachTo(Sequence sequence)` Deprecated. use `Sequence.addROI(ROI)` instead
`void`	`beginUpdate()`
`abstract boolean`	`canSetBounds()` Returns `true` if this ROI accepts bounds change through the `setBounds5D(Rectangle5D)` method.
`abstract boolean`	`canSetPosition()` Returns `true` if this ROI accepts position change through the `setPosition5D(Point5D)` method.
`static double`	`canvasToImageDeltaX(IcyCanvas canvas, int value)` Deprecated. Use `IcyCanvas` methods instead
`static double`	`canvasToImageDeltaY(IcyCanvas canvas, int value)` Deprecated. Use `IcyCanvas` methods instead
`static double`	`canvasToImageLogDeltaX(IcyCanvas canvas, double value)` Deprecated. Use `IcyCanvas` methods instead
`static double`	`canvasToImageLogDeltaX(IcyCanvas canvas, double value, double logFactor)` Deprecated. Use `IcyCanvas` methods instead
`static double`	`canvasToImageLogDeltaX(IcyCanvas canvas, int value)` Deprecated. Use `IcyCanvas` methods instead
`static double`	`canvasToImageLogDeltaX(IcyCanvas canvas, int value, double logFactor)` Deprecated. Use `IcyCanvas` methods instead
`static double`	`canvasToImageLogDeltaY(IcyCanvas canvas, double value)` Deprecated. Use `IcyCanvas` methods instead
`static double`	`canvasToImageLogDeltaY(IcyCanvas canvas, double value, double logFactor)` Deprecated. Use `IcyCanvas` methods instead
`static double`	`canvasToImageLogDeltaY(IcyCanvas canvas, int value)` Deprecated. Use `IcyCanvas` methods instead
`static double`	`canvasToImageLogDeltaY(IcyCanvas canvas, int value, double logFactor)` Deprecated. Use `IcyCanvas` methods instead
`abstract Rectangle5D`	`computeBounds5D()` Calculate and returns the bounding box of the `ROI`.
`abstract double`	`computeNumberOfContourPoints()` Compute and returns the number of point (pixel) composing the ROI contour.
`abstract double`	`computeNumberOfPoints()` Compute and returns the number of point (pixel) contained in the ROI.
`abstract boolean`	`contains(double x, double y, double z, double t, double c)` Tests if a specified 5D point is inside the ROI.
`abstract 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.
`boolean`	`contains(Point5D p)` Tests if a specified `Point5D` is inside the ROI.
`boolean`	`contains(Rectangle5D r)` Tests if the `ROI` entirely contains the specified `Rectangle5D`.
`boolean`	`contains(ROI roi)` Tests if the `ROI` entirely contains the specified `ROI`.
`boolean`	`copyFrom(ROI roi)` Copy all properties from the given ROI.
`static ROI`	`create(java.lang.String className)` Create a ROI from its class name or `PluginROI` class name.
`static ROI`	`create(java.lang.String className, java.awt.geom.Point2D imagePoint)` Deprecated. Use `create(String, Point5D)` instead
`static ROI`	`create(java.lang.String className, Point5D imagePoint)` Create a ROI from its class name or `PluginROI` class name (interactive mode).
`static ROI`	`create(java.lang.String className, Sequence seq, java.awt.geom.Point2D imagePoint, boolean creation)` Deprecated. Use `create(String, Point5D)` instead.
`static ROI`	`createFromXML(org.w3c.dom.Node node)` Create a ROI from a xml definition
`void`	`delete()` Deprecated. Use `remove()` instead.
`void`	`delete(boolean canUndo)` Deprecated. Use `remove(boolean)` instead.
`void`	`detachFrom(Sequence sequence)` Deprecated. use `Sequence.removeROI(ROI)` instead
`void`	`detachFromAll()` Deprecated. Use `remove()` instead.
`void`	`detachFromAll(boolean canUndo)` Deprecated. Use `remove(boolean)` instead.
`void`	`endUpdate()`
`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.
`void`	`focusChanged()` Called when ROI focus state changed.
`double`	`getAdjustedStroke(IcyCanvas canvas)` Get adjusted stroke for the current canvas transformation
`static double`	`getAdjustedStroke(IcyCanvas canvas, double stroke)`
`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.
`boolean[]`	`getBooleanMask2D(java.awt.Rectangle rect, int z, int t, int c, boolean inclusive)` Get the boolean bitmap mask for the specified rectangular area of the roi and for the specified Z,T position.
`Rectangle5D`	`getBounds5D()` Returns the bounding box of the `ROI`.
`java.lang.String`	`getClassName()`
`java.awt.Color`	`getColor()` Return the ROI painter base color.
`ROI`	`getCopy()` Returns a copy of the ROI or `null` if the operation failed.
`static java.awt.Color`	`getDefaultColor()`
`java.lang.String`	`getDefaultName()`
`static float`	`getDefaultOpacity()`
`static boolean`	`getDefaultShowName()`
`static double`	`getDefaultStroke()`
`abstract int`	`getDimension()` Returns the number of dimension of the ROI: 2 for ROI2D 3 for ROI3D 4 for ROI4D 5 for ROI5D
`java.awt.Color`	`getDisplayColor()` Returns the color used to display the ROI depending its current state.
`ROI`	`getExclusiveUnion(ROI roi)` Compute exclusive union with specified `ROI` and return result in a new `ROI`.
`Sequence`	`getFirstSequence()` Return first sequence where ROI is attached
`java.awt.Color`	`getFocusedColor()` Return the ROI painter focused color.
`ROI.ROIGroupId`	`getGroupId()`
`java.awt.Image`	`getIcon()`
`int`	`getId()` ROI unique id
`ROI`	`getIntersection(ROI roi)` Compute intersection with specified `ROI` and return result in a new `ROI`.
`double`	`getLength(Sequence sequence)` Computes and returns the length/perimeter of the ROI in um given the pixel size informations from the specified Sequence.
`java.lang.String`	`getName()`
`static java.lang.String`	`getNameSuffix(int z, int t, int c)` Returns the name suffix when we want to obtain only a sub part of the ROI (always in Z,T,C order).
`double`	`getNumberOfContourPoints()` Returns the number of point (pixel) composing the ROI contour.
`double`	`getNumberOfPoints()` Returns the number of point (pixel) contained in the ROI.
`float`	`getOpacity()` Returns the ROI painter opacity factor (0 = transparent while 1 means opaque).
`ROI.ROIPainter`	`getOverlay()` Returns the ROI overlay (used to draw and interact with `ROI` on `IcyCanvas`)
`ROI.ROIPainter`	`getPainter()` Deprecated. Use `getOverlay()` instead.
`double`	`getPerimeter()` Deprecated. Use `getLength(Sequence)` or `getNumberOfContourPoints()` instead.
`Point5D`	`getPosition5D()` Returns the ROI position which normally correspond to the minimum point of the ROI bounds.
`java.util.Map<java.lang.String,java.lang.String>`	`getProperties()` Retrieve all custom ROI properties (map of (Key,Value)).
`java.lang.String`	`getProperty(java.lang.String name)` Retrieve a ROI property value.
`java.lang.Object`	`getPropertyValue(java.lang.String propertyName)` Deprecated. use `getProperty(String)` instead.
`static int`	`getROICount(org.w3c.dom.Node node)` Return the number of ROI defined in the specified XML node.
`static java.util.ArrayList<ROI>`	`getROIList(java.util.ArrayList<? extends ROI> rois, java.lang.Class<? extends ROI> clazz)` Deprecated. Use `getROIList(List, Class)` instead.
`static java.util.List<ROI>`	`getROIList(java.util.List<? extends ROI> rois, java.lang.Class<? extends ROI> clazz)` Return ROI of specified type from the ROI list
`static java.util.List<ROI>`	`getROIList(ROI[] rois, java.lang.Class<? extends ROI> clazz)` Deprecated. Use `getROIList(List, Class)` instead.
`static java.util.List<ROI>`	`getROIsFromXML(org.w3c.dom.Node node)` Deprecated. Use `loadROIsFromXML(Node)` instead.
`java.awt.Color`	`getSelectedColor()` Deprecated.
`java.util.ArrayList<Sequence>`	`getSequences()` Return sequences where ROI is attached
`boolean`	`getShowName()` Return `true` if ROI should display its name at draw time.
`java.lang.String`	`getSimpleClassName()`
`double`	`getStroke()` Return the ROI painter stroke.
`ROI`	`getSubROI(int z, int t, int c)` Returns a sub part of the ROI.
`ROI`	`getSubtraction(ROI roi)` Subtract the specified `ROI` and return result in a new `ROI`.
`ROI`	`getUnion(ROI roi)` Compute union with specified `ROI` and return result in a new `ROI`.
`double`	`getVolume()` Deprecated. Only for ROI3D object, use `getNumberOfPoints()` instead for other type of ROI.
`abstract boolean`	`hasSelectedPoint()` Returns true if the ROI has a (control) point which is currently focused/selected
`void`	`internalFocus()`
`void`	`internalSelect()` Deprecated. Use `setSelected(boolean)` instead.
`void`	`internalUnfocus()`
`void`	`internalUnselect()` Deprecated. Use `setSelected(boolean)` instead.
`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`.
`abstract 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`	`intersects(Rectangle5D r)` Tests if the interior of the `ROI` intersects the interior of a specified rectangular area.
`boolean`	`intersects(ROI roi)` Tests if the current `ROI` intersects the specified `ROI`.
`abstract boolean`	`isActiveFor(IcyCanvas canvas)` Return true if the ROI is active for the specified canvas.
`boolean`	`isAttached(Sequence sequence)` Return true is this ROI is attached to at least one sequence
`boolean`	`isCreating()`
`boolean`	`isDefaultName()` Returns `true` if the ROI has its default name
`boolean`	`isEditable()` Deprecated. Use `isReadOnly()` instead.
`boolean`	`isEmpty()` Returns `true` if the ROI is empty (does not contains anything).
`boolean`	`isFocused()`
`boolean`	`isReadOnly()` Return true if ROI is in read only state (cannot be modified from GUI).
`boolean`	`isSelected()`
`boolean`	`isUpdating()`
`boolean`	`loadFromXML(org.w3c.dom.Node node)` LOAD
`boolean`	`loadFromXML(org.w3c.dom.Node node, boolean preserveId)`
`static java.util.List<ROI>`	`loadROIsFromXML(org.w3c.dom.Node node)` Return a list of ROI from a XML node.
`ROI`	`merge(ROI roi, ShapeUtil.BooleanOperator op)` Compute the boolean operation with specified `ROI` and return result in a new `ROI`.
`ROI`	`mergeWith(ROI roi, ShapeUtil.BooleanOperator op, boolean allowCreate)` Same as `#merge(ROI, BooleanOperator)` except it modifies the current `ROI` to reflect the result of the boolean operation with specified `ROI`.
`void`	`nameChanged()` Deprecated. Use `propertyChanged(String)` instead.
`void`	`onChanged(CollapsibleEvent object)` fire changed event
`void`	`painterChanged()` Deprecated.
`void`	`propertyChanged(java.lang.String propertyName)` Called when ROI property has changed
`void`	`remove()` Remove this ROI (detach from all sequence)
`void`	`remove(boolean canUndo)` Remove this ROI (detach from all sequence)
`void`	`removeListener(ROIListener listener)` Remove a listener
`void`	`roiChanged()` Deprecated. Use `roiChanged(boolean)` instead.
`void`	`roiChanged(boolean contentChanged)` Called when ROI has changed its content and/or position.
`void`	`roiChanged(ROIEvent.ROIPointEventType pointEventType, java.lang.Object point)` Deprecated. Use `roiChanged(boolean)` instead
`static void`	`saveROIsToXML(org.w3c.dom.Node node, java.util.List<ROI> rois)` Set a list of ROI to a XML node.
`boolean`	`saveToXML(org.w3c.dom.Node node)` SAVE
`void`	`selectionChanged()` Called when ROI selected state changed.
`abstract void`	`setBounds5D(Rectangle5D bounds)` Set the `ROI` bounds.
`void`	`setColor(java.awt.Color value)` Set the ROI painter base color.
`void`	`setCreating(boolean value)` Set the internal creation mode state.
`static void`	`setDefaultColor(java.awt.Color value)`
`static void`	`setDefaultOpacity(float value)`
`static void`	`setDefaultShowName(boolean value)`
`static void`	`setDefaultStroke(double value)`
`void`	`setEditable(boolean value)` Deprecated. Use `setReadOnly(boolean)` instead.
`void`	`setFocused(boolean value)`
`void`	`setGroupId(ROI.ROIGroupId value)`
`void`	`setIcon(java.awt.Image value)`
`void`	`setMousePos(java.awt.geom.Point2D pos)` Deprecated. Use `getOverlay().setMousePos(..)` instead.
`void`	`setName(java.lang.String value)`
`void`	`setOpacity(float value)` Sets the ROI painter content opacity factor (0 = transparent while 1 means opaque).
`abstract void`	`setPosition5D(Point5D position)` Set the `ROI` position.
`void`	`setProperty(java.lang.String name, java.lang.String value)` Generic way to set ROI property value.
`void`	`setPropertyValue(java.lang.String propertyName, java.lang.Object value)` Deprecated. use `setProperty(String, String)`
`void`	`setReadOnly(boolean value)` Set the read only state of ROI.
`static void`	`setROIsFromXML(org.w3c.dom.Node node, java.util.List<ROI> rois)` Deprecated. Use `saveROIsToXML(Node, List)` instead
`void`	`setSelected(boolean value)` Set the selected state of this ROI.
`void`	`setSelected(boolean value, boolean exclusive)` Deprecated. Use `setSelected(boolean)` or `Sequence.setSelectedROI(ROI)` depending you want exclusive selection or not.
`void`	`setSelectedColor(java.awt.Color value)` Deprecated. selected color is automatically calculated.
`void`	`setShowName(boolean value)` Set the show name property of ROI.
`void`	`setStroke(double value)` Set ROI painter stroke.
`ROI`	`subtract(ROI roi, boolean allowCreate)` Subtract the specified `ROI` content from current `ROI`.
`void`	`unselectAllPoints()` Remove focus/selected state on all (control) points.

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

- Field Detail
  - ID_ROI
```
public static final java.lang.String ID_ROI
```
    See Also:
    Constant Field Values
  - ID_CLASSNAME
```
public static final java.lang.String ID_CLASSNAME
```
    See Also:
    Constant Field Values
  - ID_ID
```
public static final java.lang.String ID_ID
```
    See Also:
    Constant Field Values
  - ID_NAME
```
public static final java.lang.String ID_NAME
```
    See Also:
    Constant Field Values
  - ID_GROUPID
```
public static final java.lang.String ID_GROUPID
```
    See Also:
    Constant Field Values
  - ID_COLOR
```
public static final java.lang.String ID_COLOR
```
    See Also:
    Constant Field Values
  - ID_STROKE
```
public static final java.lang.String ID_STROKE
```
    See Also:
    Constant Field Values
  - ID_OPACITY
```
public static final java.lang.String ID_OPACITY
```
    See Also:
    Constant Field Values
  - ID_SELECTED
```
public static final java.lang.String ID_SELECTED
```
    See Also:
    Constant Field Values
  - ID_READONLY
```
public static final java.lang.String ID_READONLY
```
    See Also:
    Constant Field Values
  - ID_SHOWNAME
```
public static final java.lang.String ID_SHOWNAME
```
    See Also:
    Constant Field Values
  - ID_PROPERTIES
```
public static final java.lang.String ID_PROPERTIES
```
    See Also:
    Constant Field Values
  - idComparator
```
public static final ROI.ROIIdComparator idComparator
```
  - nameComparator
```
public static final ROI.ROINameComparator nameComparator
```
  - DEFAULT_STROKE
```
public static final double DEFAULT_STROKE
```
    See Also:
    Constant Field Values
  - DEFAULT_COLOR
```
public static final java.awt.Color DEFAULT_COLOR
```
  - DEFAULT_OPACITY
```
public static final float DEFAULT_OPACITY
```
    See Also:
    Constant Field Values
  - defaultColor
```
public static java.awt.Color defaultColor
```
  - defaultOpacity
```
public static java.lang.Float defaultOpacity
```
  - defaultStroke
```
public static java.lang.Double defaultStroke
```
  - defaultShowName
```
public static java.lang.Boolean defaultShowName
```
  - DEFAULT_NORMAL_COLOR
```
@Deprecated
public static final java.awt.Color DEFAULT_NORMAL_COLOR
```
    Deprecated. Use DEFAULT_COLOR instead.
  - PROPERTY_NAME
```
public static final java.lang.String PROPERTY_NAME
```
    See Also:
    Constant Field Values
  - PROPERTY_GROUPID
```
public static final java.lang.String PROPERTY_GROUPID
```
    See Also:
    Constant Field Values
  - PROPERTY_ICON
```
public static final java.lang.String PROPERTY_ICON
```
    See Also:
    Constant Field Values
  - PROPERTY_CREATING
```
public static final java.lang.String PROPERTY_CREATING
```
    See Also:
    Constant Field Values
  - PROPERTY_READONLY
```
public static final java.lang.String PROPERTY_READONLY
```
    See Also:
    Constant Field Values
  - PROPERTY_SHOWNAME
```
public static final java.lang.String PROPERTY_SHOWNAME
```
    See Also:
    Constant Field Values
  - PROPERTY_COLOR
```
public static final java.lang.String PROPERTY_COLOR
```
    See Also:
    Constant Field Values
  - PROPERTY_STROKE
```
public static final java.lang.String PROPERTY_STROKE
```
    See Also:
    Constant Field Values
  - PROPERTY_OPACITY
```
public static final java.lang.String PROPERTY_OPACITY
```
    See Also:
    Constant Field Values
  - ROI_CHANGED_POSITION
```
public static final java.lang.String ROI_CHANGED_POSITION
```
    See Also:
    Constant Field Values
  - ROI_CHANGED_ALL
```
public static final java.lang.String ROI_CHANGED_ALL
```
    See Also:
    Constant Field Values
- Constructor Detail
  - ROI
```
public ROI()
```
- Method Detail
  - create
```
public static ROI create(java.lang.String className)
```
    Create a ROI from its class name or PluginROI class name.
    
    Parameters:
    className - roi class name or PluginROI class name.
    
    Returns:
    ROI (null if command is an incorrect ROI class name)
  - create
```
public static ROI create(java.lang.String className,
         Point5D imagePoint)
```
    Create a ROI from its class name or PluginROI class name (interactive mode).
    
    Parameters:
    className - roi class name or PluginROI class name.
    imagePoint - initial point position in image coordinates (interactive mode).
    
    Returns:
    ROI (null if the specified class name is an incorrect ROI class name)
  - create
```
@Deprecated
public static ROI create(java.lang.String className,
                    java.awt.geom.Point2D imagePoint)
```
    Deprecated. Use create(String, Point5D) instead
  - create
```
@Deprecated
public static ROI create(java.lang.String className,
                    Sequence seq,
                    java.awt.geom.Point2D imagePoint,
                    boolean creation)
```
    Deprecated. Use create(String, Point5D) instead.
  - createFromXML
```
public static ROI createFromXML(org.w3c.dom.Node node)
```
    Create a ROI from a xml definition
    
    Parameters:
    node - xml node defining the roi
    
    Returns:
    ROI (null if node is an incorrect ROI definition)
  - getAdjustedStroke
```
public static double getAdjustedStroke(IcyCanvas canvas,
                       double stroke)
```
  - getROIList
```
public static java.util.List<ROI> getROIList(java.util.List<? extends ROI> rois,
                             java.lang.Class<? extends ROI> clazz)
```
    Return ROI of specified type from the ROI list
  - getROIList
```
@Deprecated
public static java.util.ArrayList<ROI> getROIList(java.util.ArrayList<? extends ROI> rois,
                                             java.lang.Class<? extends ROI> clazz)
```
    Deprecated. Use getROIList(List, Class) instead.
  - getROIList
```
@Deprecated
public static java.util.List<ROI> getROIList(ROI[] rois,
                                        java.lang.Class<? extends ROI> clazz)
```
    Deprecated. Use getROIList(List, Class) instead.
  - getROICount
```
public static int getROICount(org.w3c.dom.Node node)
```
    Return the number of ROI defined in the specified XML node.
    
    Parameters:
    node - XML node defining the ROI list
    
    Returns:
    the number of ROI defined in the XML node.
  - loadROIsFromXML
```
public static java.util.List<ROI> loadROIsFromXML(org.w3c.dom.Node node)
```
    Return a list of ROI from a XML node.
    
    Parameters:
    node - XML node defining the ROI list
    
    Returns:
    a list of ROI
  - getROIsFromXML
```
@Deprecated
public static java.util.List<ROI> getROIsFromXML(org.w3c.dom.Node node)
```
    Deprecated. Use loadROIsFromXML(Node) instead.
  - saveROIsToXML
```
public static void saveROIsToXML(org.w3c.dom.Node node,
                 java.util.List<ROI> rois)
```
    Set a list of ROI to a XML node.
    
    Parameters:
    node - XML node which is used to store the list of ROI
    rois - the list of ROI to store in the XML node
  - setROIsFromXML
```
@Deprecated
public static void setROIsFromXML(org.w3c.dom.Node node,
                             java.util.List<ROI> rois)
```
    Deprecated. Use saveROIsToXML(Node, List) instead
  - getDefaultColor
```
public static java.awt.Color getDefaultColor()
```
  - getDefaultOpacity
```
public static float getDefaultOpacity()
```
  - getDefaultStroke
```
public static double getDefaultStroke()
```
  - getDefaultShowName
```
public static boolean getDefaultShowName()
```
  - setDefaultColor
```
public static void setDefaultColor(java.awt.Color value)
```
  - setDefaultOpacity
```
public static void setDefaultOpacity(float value)
```
  - setDefaultStroke
```
public static void setDefaultStroke(double value)
```
  - setDefaultShowName
```
public static void setDefaultShowName(boolean value)
```
  - canvasToImageDeltaX
```
@Deprecated
public static double canvasToImageDeltaX(IcyCanvas canvas,
                                    int value)
```
    Deprecated. Use IcyCanvas methods instead
  - canvasToImageLogDeltaX
```
@Deprecated
public static double canvasToImageLogDeltaX(IcyCanvas canvas,
                                       double value,
                                       double logFactor)
```
    Deprecated. Use IcyCanvas methods instead
  - canvasToImageLogDeltaX
```
@Deprecated
public static double canvasToImageLogDeltaX(IcyCanvas canvas,
                                       double value)
```
    Deprecated. Use IcyCanvas methods instead
  - canvasToImageLogDeltaX
```
@Deprecated
public static double canvasToImageLogDeltaX(IcyCanvas canvas,
                                       int value,
                                       double logFactor)
```
    Deprecated. Use IcyCanvas methods instead
  - canvasToImageLogDeltaX
```
@Deprecated
public static double canvasToImageLogDeltaX(IcyCanvas canvas,
                                       int value)
```
    Deprecated. Use IcyCanvas methods instead
  - canvasToImageDeltaY
```
@Deprecated
public static double canvasToImageDeltaY(IcyCanvas canvas,
                                    int value)
```
    Deprecated. Use IcyCanvas methods instead
  - canvasToImageLogDeltaY
```
@Deprecated
public static double canvasToImageLogDeltaY(IcyCanvas canvas,
                                       double value,
                                       double logFactor)
```
    Deprecated. Use IcyCanvas methods instead
  - canvasToImageLogDeltaY
```
@Deprecated
public static double canvasToImageLogDeltaY(IcyCanvas canvas,
                                       double value)
```
    Deprecated. Use IcyCanvas methods instead
  - canvasToImageLogDeltaY
```
@Deprecated
public static double canvasToImageLogDeltaY(IcyCanvas canvas,
                                       int value,
                                       double logFactor)
```
    Deprecated. Use IcyCanvas methods instead
  - canvasToImageLogDeltaY
```
@Deprecated
public static double canvasToImageLogDeltaY(IcyCanvas canvas,
                                       int value)
```
    Deprecated. Use IcyCanvas methods instead
  - getDimension
```
public abstract int getDimension()
```
    Returns the number of dimension of the ROI:
    2 for ROI2D
    3 for ROI3D
    4 for ROI4D
    5 for ROI5D
  - attachTo
```
@Deprecated
public void attachTo(Sequence sequence)
```
    Deprecated. use Sequence.addROI(ROI) instead
  - detachFrom
```
@Deprecated
public void detachFrom(Sequence sequence)
```
    Deprecated. use Sequence.removeROI(ROI) instead
  - detachFromAll
```
@Deprecated
public void detachFromAll(boolean canUndo)
```
    Deprecated. Use remove(boolean) instead.
  - detachFromAll
```
@Deprecated
public void detachFromAll()
```
    Deprecated. Use remove() instead.
  - isAttached
```
public boolean isAttached(Sequence sequence)
```
    Return true is this ROI is attached to at least one sequence
  - getFirstSequence
```
public Sequence getFirstSequence()
```
    Return first sequence where ROI is attached
  - getSequences
```
public java.util.ArrayList<Sequence> getSequences()
```
    Return sequences where ROI is attached
  - remove
```
public void remove(boolean canUndo)
```
    Remove this ROI (detach from all sequence)
  - remove
```
public void remove()
```
    Remove this ROI (detach from all sequence)
  - delete
```
@Deprecated
public void delete(boolean canUndo)
```
    Deprecated. Use remove(boolean) instead.
  - delete
```
@Deprecated
public void delete()
```
    Deprecated. Use remove() instead.
  - getClassName
```
public java.lang.String getClassName()
```
  - getSimpleClassName
```
public java.lang.String getSimpleClassName()
```
  - getId
```
public int getId()
```
    ROI unique id
  - getPainter
```
@Deprecated
public ROI.ROIPainter getPainter()
```
    Deprecated. Use getOverlay() instead.
  - getOverlay
```
public ROI.ROIPainter getOverlay()
```
    Returns the ROI overlay (used to draw and interact with ROI on IcyCanvas)
  - getStroke
```
public double getStroke()
```
    Return the ROI painter stroke.
  - getAdjustedStroke
```
public double getAdjustedStroke(IcyCanvas canvas)
```
    Get adjusted stroke for the current canvas transformation
  - setStroke
```
public void setStroke(double value)
```
    Set ROI painter stroke.
  - getOpacity
```
public float getOpacity()
```
    Returns the ROI painter opacity factor (0 = transparent while 1 means opaque).
  - setOpacity
```
public void setOpacity(float value)
```
    Sets the ROI painter content opacity factor (0 = transparent while 1 means opaque).
  - getFocusedColor
```
public java.awt.Color getFocusedColor()
```
    Return the ROI painter focused color.
  - getSelectedColor
```
@Deprecated
public java.awt.Color getSelectedColor()
```
    Deprecated.
  - getDisplayColor
```
public java.awt.Color getDisplayColor()
```
    Returns the color used to display the ROI depending its current state.
  - getColor
```
public java.awt.Color getColor()
```
    Return the ROI painter base color.
  - setColor
```
public void setColor(java.awt.Color value)
```
    Set the ROI painter base color.
  - setSelectedColor
```
@Deprecated
public void setSelectedColor(java.awt.Color value)
```
    Deprecated. selected color is automatically calculated.
  - getIcon
```
public java.awt.Image getIcon()
```
    Returns:
    the icon
  - setIcon
```
public void setIcon(java.awt.Image value)
```
    Parameters:
    value - the icon to set
  - getGroupId
```
public ROI.ROIGroupId getGroupId()
```
    Returns:
    the group id
  - setGroupId
```
public void setGroupId(ROI.ROIGroupId value)
```
    Parameters:
    value - the group id to set
  - getDefaultName
```
public java.lang.String getDefaultName()
```
    Returns:
    the default name for this ROI class
  - isDefaultName
```
public boolean isDefaultName()
```
    Returns true if the ROI has its default name
  - getName
```
public java.lang.String getName()
```
    Returns:
    the name
  - setName
```
public void setName(java.lang.String value)
```
    Parameters:
    value - the name to set
  - getProperties
```
public java.util.Map<java.lang.String,java.lang.String> getProperties()
```
    Retrieve all custom ROI properties (map of (Key,Value)).
  - getProperty
```
public java.lang.String getProperty(java.lang.String name)
```
    Retrieve a ROI property value.
    Returns null if the property value is empty.
    
    Parameters:
    name - Property name.
    Note that it can be default property name (as "readOnly") in which case the value will be returned in String format if possible or launch an IllegalArgumentException when not possible.
  - setProperty
```
public void setProperty(java.lang.String name,
               java.lang.String value)
```
    Generic way to set ROI property value.
    
    Parameters:
    name - Property name.
    Note that it can be default property name (as "readOnly") in which case the value will be set in String format if possible or launch an IllegalArgumentException when not possible.
    value - the value to set in the property (for instance "FALSE" for PROPERTY_READONLY)
  - getPropertyValue
```
@Deprecated
public java.lang.Object getPropertyValue(java.lang.String propertyName)
```
    Deprecated. use getProperty(String) instead.
  - setPropertyValue
```
@Deprecated
public void setPropertyValue(java.lang.String propertyName,
                               java.lang.Object value)
```
    Deprecated. use setProperty(String, String)
  - isCreating
```
public boolean isCreating()
```
    Returns:
    the creating
  - setCreating
```
public void setCreating(boolean value)
```
    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.
  - hasSelectedPoint
```
public abstract boolean hasSelectedPoint()
```
    Returns true if the ROI has a (control) point which is currently focused/selected
  - unselectAllPoints
```
public void unselectAllPoints()
```
    Remove focus/selected state on all (control) points.
    Override this method depending implementation
  - isFocused
```
public boolean isFocused()
```
    Returns:
    the focused
  - setFocused
```
public void setFocused(boolean value)
```
    Parameters:
    value - the focused to set
  - internalFocus
```
public void internalFocus()
```
  - internalUnfocus
```
public void internalUnfocus()
```
  - isSelected
```
public boolean isSelected()
```
    Returns:
    the selected
  - setSelected
```
public void setSelected(boolean value)
```
    Set the selected state of this ROI.
    Use Sequence.setSelectedROI(ROI) for exclusive ROI selection.
    
    Parameters:
    value - the selected to set
  - setSelected
```
@Deprecated
public void setSelected(boolean value,
                          boolean exclusive)
```
    Deprecated. Use setSelected(boolean) or Sequence.setSelectedROI(ROI) depending you want exclusive selection or not.
  - internalUnselect
```
@Deprecated
public void internalUnselect()
```
    Deprecated. Use setSelected(boolean) instead.
  - internalSelect
```
@Deprecated
public void internalSelect()
```
    Deprecated. Use setSelected(boolean) instead.
  - isEditable
```
@Deprecated
public boolean isEditable()
```
    Deprecated. Use isReadOnly() instead.
  - setEditable
```
@Deprecated
public void setEditable(boolean value)
```
    Deprecated. Use setReadOnly(boolean) instead.
  - isReadOnly
```
public boolean isReadOnly()
```
    Return true if ROI is in read only state (cannot be modified from GUI).
  - setReadOnly
```
public void setReadOnly(boolean value)
```
    Set the read only state of ROI.
  - getShowName
```
public boolean getShowName()
```
    Return true if ROI should display its name at draw time.
  - setShowName
```
public void setShowName(boolean value)
```
    Set the show name property of ROI.
    When set to true the ROI shows its name at draw time.
  - isActiveFor
```
public abstract boolean isActiveFor(IcyCanvas canvas)
```
    Return true if the ROI is active for the specified canvas.
  - computeBounds5D
```
public abstract Rectangle5D computeBounds5D()
```
    Calculate and returns the bounding box of the ROI.
    This method is used by getBounds5D() which should try to cache the result as the bounding box calculation can take some computation time for complex ROI.
  - getBounds5D
```
public Rectangle5D getBounds5D()
```
    Returns the bounding box of the ROI. Note that there is no guarantee that the returned Rectangle5D is the smallest bounding box that encloses the ROI, only that the ROI lies entirely within the indicated Rectangle5D.
    
    Returns:
    an instance of Rectangle5D that is a bounding box of the ROI.
    See Also:
    computeBounds5D()
  - getPosition5D
```
public Point5D getPosition5D()
```
    Returns the ROI position which normally correspond to the minimum point of the ROI bounds.
    
    See Also:
    getBounds5D()
  - canSetBounds
```
public abstract boolean canSetBounds()
```
    Returns true if this ROI accepts bounds change through the setBounds5D(Rectangle5D) method.
  - canSetPosition
```
public abstract boolean canSetPosition()
```
    Returns true if this ROI accepts position change through the setPosition5D(Point5D) method.
  - setBounds5D
```
public abstract void setBounds5D(Rectangle5D bounds)
```
    Set the ROI bounds.
    Note that not all ROI supports bounds modification and you should call canSetBounds() first to test if the operation is supported.
    
    Parameters:
    bounds - new ROI bounds
  - setPosition5D
```
public abstract void setPosition5D(Point5D position)
```
    Set the ROI position.
    Note that not all ROI supports position modification and you should call canSetPosition() first to test if the operation is supported.
    
    Parameters:
    position - new ROI position
  - isEmpty
```
public boolean isEmpty()
```
    Returns true if the ROI is empty (does not contains anything).
  - contains
```
public abstract boolean contains(double x,
               double y,
               double z,
               double t,
               double c)
```
    Tests if a specified 5D point is inside the ROI.
    
    Returns:
    true if the specified Point5D is inside the boundary of the ROI; false otherwise.
  - contains
```
public boolean contains(Point5D p)
```
    Tests if a specified Point5D is inside the ROI.
    
    Parameters:
    p - the specified Point5D to be tested
    
    Returns:
    true if the specified Point2D is inside the boundary of the ROI; false otherwise.
  - contains
```
public abstract 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. 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.
    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.
  - contains
```
public boolean contains(Rectangle5D r)
```
    Tests if the ROI entirely contains the specified Rectangle5D. The ROI.contains() method allows a implementation to conservatively return false when:
    - the intersect method returns true and
    - the calculations to determine whether or not the ROI entirely contains the Rectangle2D are prohibitively expensive.
    This means that for some ROIs this method might return false even though the ROI contains the Rectangle5D.
    Parameters:
    r - The specified Rectangle5D
    
    Returns:
    true if the interior of the ROI entirely contains the Rectangle5D; false otherwise or, if the ROI contains the Rectangle5D and the intersects method returns true and the containment calculations would be too expensive to perform.
    See Also:
    contains(double, double, double, double, double, double, double, double, double, double)
  - contains
```
public boolean contains(ROI roi)
```
    Tests if the ROI entirely contains the specified ROI. WARNING: this method may be "pixel accurate" only depending the internal implementation.
    
    Returns:
    true if the current ROI entirely contains the specified ROI; false otherwise.
  - intersects
```
public abstract 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. 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.
    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.
  - intersects
```
public boolean intersects(Rectangle5D r)
```
    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.
    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.
  - intersects
```
public boolean intersects(ROI roi)
```
    Tests if the current ROI intersects the specified ROI.
    Note that this method may be "pixel accurate" only depending the internal implementation.
    
    Returns:
    true if ROI intersect, false otherwise.
  - getBooleanMask2D
```
public 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.
    
    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
    
    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 boolean[] getBooleanMask2D(java.awt.Rectangle rect,
                         int z,
                         int t,
                         int c,
                         boolean inclusive)
```
    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] = false
    
    Parameters:
    rect - 2D rectangular area we want to retrieve the boolean mask
    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.
  - getBooleanMask2D
```
public 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.
    
    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
    
    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.
  - mergeWith
```
public ROI mergeWith(ROI roi,
            ShapeUtil.BooleanOperator op,
            boolean allowCreate)
              throws java.lang.UnsupportedOperationException
```
    Same as #merge(ROI, BooleanOperator) except it modifies the current ROI to reflect the result of the boolean operation with specified 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.
    
    Parameters:
    roi - the ROI to merge with current ROI
    op - the boolean operation to process
    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 merged together.
    See Also:
    #merge(ROI, BooleanOperator)
  - add
```
public ROI add(ROI roi,
      boolean allowCreate)
        throws java.lang.UnsupportedOperationException
```
    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)
 
     ################     ################     ################
     ##############         ##############     ################
     ############             ############     ################
     ##########                 ##########     ################
     ########                     ########     ################
     ######                         ######     ######    ######
     ####                             ####     ####        ####
     ##                                 ##     ##            ##
 
```
    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:
    getUnion(ROI)
  - intersect
```
public ROI intersect(ROI roi,
            boolean allowCreate)
              throws java.lang.UnsupportedOperationException
```
    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)
 
     ################     ################     ################
     ##############         ##############       ############
     ############             ############         ########
     ##########                 ##########           ####
     ########                     ########
     ######                         ######
     ####                             ####
     ##                                 ##
 
```
    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:
    getIntersection(ROI)
  - exclusiveAdd
```
public ROI exclusiveAdd(ROI roi,
               boolean allowCreate)
                 throws java.lang.UnsupportedOperationException
```
    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)
 
     ################     ################
     ##############         ##############     ##            ##
     ############             ############     ####        ####
     ##########                 ##########     ######    ######
     ########                     ########     ################
     ######                         ######     ######    ######
     ####                             ####     ####        ####
     ##                                 ##     ##            ##
 
```
    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:
    getExclusiveUnion(ROI)
  - subtract
```
public ROI subtract(ROI roi,
           boolean allowCreate)
             throws java.lang.UnsupportedOperationException
```
    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.
    
    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:
    getSubtraction(ROI)
  - merge
```
public ROI merge(ROI roi,
        ShapeUtil.BooleanOperator op)
          throws java.lang.UnsupportedOperationException
```
    Compute the boolean operation with specified ROI and return result in a new ROI.
    
    Throws:
    
    java.lang.UnsupportedOperationException
  - getUnion
```
public ROI getUnion(ROI roi)
             throws java.lang.UnsupportedOperationException
```
    Compute union with specified ROI and return result in a new ROI.
    The default implementation use ROIUtil.getUnion(ROI, ROI) internally but it maybe overridden.
    
    Throws:
    
    java.lang.UnsupportedOperationException
  - getIntersection
```
public ROI getIntersection(ROI roi)
                    throws java.lang.UnsupportedOperationException
```
    Compute intersection with specified ROI and return result in a new ROI.
    The default implementation use ROIUtil.getIntersection(ROI, ROI) internally but it maybe overridden.
    
    Throws:
    
    java.lang.UnsupportedOperationException
  - getExclusiveUnion
```
public ROI getExclusiveUnion(ROI roi)
                      throws java.lang.UnsupportedOperationException
```
    Compute exclusive union with specified ROI and return result in a new ROI.
    The default implementation use ROIUtil.getExclusiveUnion(ROI, ROI) internally but it maybe overridden.
    
    Throws:
    
    java.lang.UnsupportedOperationException
  - getSubtraction
```
public ROI getSubtraction(ROI roi)
                   throws java.lang.UnsupportedOperationException
```
    Subtract the specified ROI and return result in a new ROI.
    The default implementation use ROIUtil.getSubtraction(ROI, ROI) internally but it maybe overridden.
    
    Throws:
    
    java.lang.UnsupportedOperationException
  - computeNumberOfContourPoints
```
public abstract double computeNumberOfContourPoints()
```
    Compute and returns the number of point (pixel) composing the ROI contour.
  - getNumberOfContourPoints
```
public double getNumberOfContourPoints()
```
    Returns the number of point (pixel) composing the ROI contour.
    It is used to calculate the perimeter (2D) or surface area (3D) of the ROI.
    
    See Also:
    computeNumberOfContourPoints()
  - computeNumberOfPoints
```
public abstract double computeNumberOfPoints()
```
    Compute and returns the number of point (pixel) contained in the ROI.
  - getNumberOfPoints
```
public double getNumberOfPoints()
```
    Returns the number of point (pixel) contained in the ROI.
    It is used to calculate the area (2D) or volume (3D) of the ROI.
  - getLength
```
public double getLength(Sequence sequence)
                 throws java.lang.UnsupportedOperationException
```
    Computes and returns the length/perimeter of the ROI in um given the pixel size informations from the specified Sequence.
    Generic implementation of length computation uses the number of contour point (approximation). This method should be overridden whenever possible to provide faster and accurate calculation.
    Throws a UnsupportedOperationException if the operation is not supported for this ROI.
    
    Throws:
    
    java.lang.UnsupportedOperationException
    See Also:
    getNumberOfContourPoints()
  - getPerimeter
```
@Deprecated
public double getPerimeter()
```
    Deprecated. Use getLength(Sequence) or getNumberOfContourPoints() instead.
  - getVolume
```
@Deprecated
public double getVolume()
```
    Deprecated. Only for ROI3D object, use getNumberOfPoints() instead for other type of ROI.
  - setMousePos
```
@Deprecated
public void setMousePos(java.awt.geom.Point2D pos)
```
    Deprecated. Use getOverlay().setMousePos(..) instead.
  - getCopy
```
public ROI getCopy()
```
    Returns a copy of the ROI or null if the operation failed.
  - getNameSuffix
```
public static java.lang.String getNameSuffix(int z,
                             int t,
                             int c)
```
    Returns the name suffix when we want to obtain only a sub part of the ROI (always in Z,T,C order).
    For instance if we use for z=1, t=5 and c=-1 this method will return [Z=1, T=5]
    
    Parameters:
    z - the specific Z position (slice) we want to retrieve (-1 to retrieve the whole ROI Z dimension)
    t - the specific T position (frame) we want to retrieve (-1 to retrieve the whole ROI T dimension)
    c - the specific C position (channel) we want to retrieve (-1 to retrieve the whole ROI C dimension)
  - getSubROI
```
public ROI getSubROI(int z,
            int t,
            int c)
```
    Returns a sub part of the ROI.
    The default implementation returns result in "area" format: (ROI2DArea, ROI3DArea, ROI4DArea or ROI5DArea) where only internals pixels are preserved.
    Note that this function can eventually return null when the result ROI is empty.
    
    Parameters:
    z - the specific Z position (slice) we want to retrieve (-1 to retrieve the whole ROI Z dimension)
    t - the specific T position (frame) we want to retrieve (-1 to retrieve the whole ROI T dimension)
    c - the specific C position (channel) we want to retrieve (-1 to retrieve the whole ROI C dimension)
  - copyFrom
```
public boolean copyFrom(ROI roi)
```
    Copy all properties from the given ROI.
    All compatible properties from the source ROI are copied into current ROI except the internal id.
    Return false if the operation failed
  - loadFromXML
```
public boolean loadFromXML(org.w3c.dom.Node node,
                  boolean preserveId)
```
  - loadFromXML
```
public boolean loadFromXML(org.w3c.dom.Node node)
```
    Description copied from interface: XMLPersistent
    
    LOAD
    
    Specified by:
    
    loadFromXML in interface XMLPersistent
  - saveToXML
```
public boolean saveToXML(org.w3c.dom.Node node)
```
    Description copied from interface: XMLPersistent
    
    SAVE
    
    Specified by:
    
    saveToXML in interface XMLPersistent
  - roiChanged
```
@Deprecated
public void roiChanged(ROIEvent.ROIPointEventType pointEventType,
                         java.lang.Object point)
```
    Deprecated. Use roiChanged(boolean) instead
  - roiChanged
```
public void roiChanged(boolean contentChanged)
```
    Called when ROI has changed its content and/or position.
    
    Parameters:
    contentChanged - mean that ROI content has changed otherwise we consider only a position change
  - roiChanged
```
@Deprecated
public void roiChanged()
```
    Deprecated. Use roiChanged(boolean) instead.
  - selectionChanged
```
public void selectionChanged()
```
    Called when ROI selected state changed.
  - focusChanged
```
public void focusChanged()
```
    Called when ROI focus state changed.
  - painterChanged
```
@Deprecated
public void painterChanged()
```
    Deprecated.
    
    Called when ROI painter changed.
  - nameChanged
```
@Deprecated
public void nameChanged()
```
    Deprecated. Use propertyChanged(String) instead.
    
    Called when ROI name has changed.
  - propertyChanged
```
public void propertyChanged(java.lang.String propertyName)
```
    Called when ROI property has changed
  - addListener
```
public void addListener(ROIListener listener)
```
    Add a listener
    
    Parameters:
    listener -
  - removeListener
```
public void removeListener(ROIListener listener)
```
    Remove a listener
    
    Parameters:
    listener -
  - beginUpdate
```
public void beginUpdate()
```
  - endUpdate
```
public void endUpdate()
```
  - isUpdating
```
public boolean isUpdating()
```
  - onChanged
```
public void onChanged(CollapsibleEvent object)
```
    Description copied from interface: ChangeListener
    
    fire changed event
    
    Specified by:
    
    onChanged in interface ChangeListener

Class ROI

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

ID_ROI

ID_CLASSNAME

ID_ID

ID_NAME

ID_GROUPID

ID_COLOR

ID_STROKE

ID_OPACITY

ID_SELECTED

ID_READONLY

ID_SHOWNAME

ID_PROPERTIES

idComparator

nameComparator

DEFAULT_STROKE

DEFAULT_COLOR

DEFAULT_OPACITY

defaultColor

defaultOpacity

defaultStroke

defaultShowName

DEFAULT_NORMAL_COLOR

PROPERTY_NAME

PROPERTY_GROUPID

PROPERTY_ICON

PROPERTY_CREATING

PROPERTY_READONLY

PROPERTY_SHOWNAME

PROPERTY_COLOR

PROPERTY_STROKE

PROPERTY_OPACITY

ROI_CHANGED_POSITION

ROI_CHANGED_ALL

Constructor Detail

ROI

Method Detail

create

create

create

create

createFromXML

getAdjustedStroke

getROIList

getROIList

getROIList

getROICount

loadROIsFromXML

getROIsFromXML

saveROIsToXML

setROIsFromXML

getDefaultColor

getDefaultOpacity

getDefaultStroke

getDefaultShowName

setDefaultColor

setDefaultOpacity

setDefaultStroke

setDefaultShowName

canvasToImageDeltaX

canvasToImageLogDeltaX

canvasToImageLogDeltaX

canvasToImageLogDeltaX

canvasToImageLogDeltaX

canvasToImageDeltaY

canvasToImageLogDeltaY

canvasToImageLogDeltaY

canvasToImageLogDeltaY

canvasToImageLogDeltaY

getDimension

attachTo

detachFrom

detachFromAll

detachFromAll