icy.roi

Class ROI5D

java.lang.Object

icy.roi.ROI

icy.roi.ROI5D

All Implemented Interfaces:

ChangeListener, XMLPersistent

Direct Known Subclasses:

ROI5DStack

public abstract class ROI5D
extends ROI

5D ROI base class.

Nested Class Summary

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

ROI.ROIGroupId, ROI.ROIIdComparator, ROI.ROINameComparator, ROI.ROIPainter

Field Summary

Fields inherited from class icy.roi.ROI

DEFAULT_COLOR, DEFAULT_NORMAL_COLOR, DEFAULT_OPACITY, DEFAULT_STROKE, defaultColor, defaultOpacity, defaultShowName, defaultStroke, ID_CLASSNAME, ID_COLOR, ID_GROUPID, ID_ID, ID_NAME, ID_OPACITY, ID_PROPERTIES, ID_READONLY, ID_ROI, ID_SELECTED, ID_SHOWNAME, ID_STROKE, idComparator, nameComparator, PROPERTY_COLOR, PROPERTY_CREATING, PROPERTY_GROUPID, PROPERTY_ICON, PROPERTY_NAME, PROPERTY_OPACITY, PROPERTY_READONLY, PROPERTY_SHOWNAME, PROPERTY_STROKE, ROI_CHANGED_ALL, ROI_CHANGED_POSITION

Constructor Summary

Constructors

Constructor and Description
ROI5D()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	canSetBounds() Returns true if this ROI accepts bounds change through the ROI.setBounds5D(Rectangle5D) method.
boolean	canSetPosition() Returns true if this ROI accepts position change through the ROI.setPosition5D(Point5D) method.
boolean	canTranslate() Returns true if the ROI support translate operation.
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(ROI roi) Tests if the ROI entirely contains the specified ROI.
BooleanMask5D	getBooleanMask(boolean inclusive) Get the BooleanMask5D object representing the roi.
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.
BooleanMask3D	getBooleanMask3D(int t, int c, boolean inclusive) Returns the BooleanMask3D object representing the XYZ volume content at specified T, C position.
BooleanMask3D	getBooleanMask3D(int z, int t, int c, boolean inclusive) Returns the BooleanMask3D object representing the XYZ volume content at specified Z, T, C position.
BooleanMask4D	getBooleanMask4D(int c, boolean inclusive) Get the BooleanMask4D object representing the roi for specified C position.
BooleanMask4D	getBooleanMask4D(int z, int t, int c, boolean inclusive) Returns the BooleanMask4D object representing the XYZT space content at specified Z and C position.
BooleanMask5D	getBooleanMask5D(int z, int t, int c, boolean inclusive) Returns the BooleanMask5D object representing the XYZTC space content at specified Z, T, C position.
Rectangle5D.Integer	getBounds() Returns an integer Rectangle5D that completely encloses the ROI.
java.lang.String	getDefaultName()
int	getDimension() Returns the number of dimension of the ROI: 2 for ROI2D 3 for ROI3D 4 for ROI4D 5 for ROI5D
Point5D.Integer	getPosition() Returns the integer ROI position which normally correspond to the minimum point of the ROI bounds.
static java.util.ArrayList<ROI5D>	getROI5DList(java.util.ArrayList<ROI> rois) Deprecated. Use getROI5DList(List) instead.
static java.util.List<ROI5D>	getROI5DList(java.util.List<ROI> rois) Return all 5D ROI from the ROI list
boolean	intersects(ROI roi) Tests if the current ROI intersects the specified ROI.
boolean	isActiveFor(IcyCanvas canvas) Return true if the ROI is active for the specified canvas.
void	setBounds5D(Rectangle5D bounds) Set the ROI bounds.
void	setPosition5D(Point5D position) Set the ROI position.
void	translate(double dx, double dy, double dz, double dt, double dc) Translate the ROI position by the specified delta X/Y/Z/T.

Methods inherited from class icy.roi.ROI

add, addListener, attachTo, beginUpdate, canvasToImageDeltaX, canvasToImageDeltaY, canvasToImageLogDeltaX, canvasToImageLogDeltaX, canvasToImageLogDeltaX, canvasToImageLogDeltaX, canvasToImageLogDeltaY, canvasToImageLogDeltaY, canvasToImageLogDeltaY, canvasToImageLogDeltaY, computeBounds5D, contains, contains, contains, contains, copyFrom, create, create, create, create, createFromXML, delete, delete, detachFrom, detachFromAll, detachFromAll, endUpdate, exclusiveAdd, focusChanged, getAdjustedStroke, getAdjustedStroke, getBooleanMask2D, 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, hasSelectedPoint, internalFocus, internalSelect, internalUnfocus, internalUnselect, intersect, intersects, intersects, isAttached, isCreating, isDefaultName, isEditable, isEmpty, isFocused, isReadOnly, isSelected, isUpdating, loadFromXML, loadFromXML, loadROIsFromXML, merge, mergeWith, nameChanged, onChanged, painterChanged, propertyChanged, remove, remove, removeListener, roiChanged, roiChanged, roiChanged, saveROIsToXML, saveToXML, selectionChanged, setColor, setCreating, setDefaultColor, setDefaultOpacity, setDefaultShowName, setDefaultStroke, setEditable, setFocused, setGroupId, setIcon, setMousePos, setName, setOpacity, setProperty, setPropertyValue, setReadOnly, setROIsFromXML, setSelected, setSelected, setSelectedColor, setShowName, setStroke, subtract, unselectAllPoints

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ROI5D

public ROI5D()

Method Detail

getROI5DList

@Deprecated
public static java.util.ArrayList<ROI5D> getROI5DList(java.util.ArrayList<ROI> rois)

Deprecated. Use getROI5DList(List) instead.

getROI5DList

public static java.util.List<ROI5D> getROI5DList(java.util.List<ROI> rois)

Return all 5D ROI from the ROI list

getDefaultName

public java.lang.String getDefaultName()

Overrides:

getDefaultName in class ROI

Returns:

the default name for this ROI class

getDimension

public final int getDimension()

Description copied from class: ROI

Returns the number of dimension of the ROI:
2 for ROI2D
3 for ROI3D
4 for ROI4D
5 for ROI5D

Specified by:

getDimension in class ROI

isActiveFor

public boolean isActiveFor(IcyCanvas canvas)

Description copied from class: ROI

Return true if the ROI is active for the specified canvas.

Specified by:

isActiveFor in class ROI

getBounds

public Rectangle5D.Integer getBounds()

Returns an integer Rectangle5D that completely encloses 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. The returned Rectangle5D might also fail to completely enclose the ROI if the ROI overflows the limited range of the integer data type. The getBounds5D method generally returns a tighter bounding box due to its greater flexibility in representation.

Returns:

an integer Rectangle5D that completely encloses the ROI.

getPosition

public Point5D.Integer getPosition()

Returns the integer ROI position which normally correspond to the minimum point of the ROI bounds.

See Also:

getBounds()

canSetBounds

public boolean canSetBounds()

Description copied from class: ROI

Returns true if this ROI accepts bounds change through the ROI.setBounds5D(Rectangle5D) method.

Specified by:

canSetBounds in class ROI

setBounds5D

public void setBounds5D(Rectangle5D bounds)

Description copied from class: ROI

Set the ROI bounds.
Note that not all ROI supports bounds modification and you should call ROI.canSetBounds() first to test if the operation is supported.

Specified by:

setBounds5D in class ROI

Parameters:

bounds - new ROI bounds

canSetPosition

public boolean canSetPosition()

Description copied from class: ROI

Returns true if this ROI accepts position change through the ROI.setPosition5D(Point5D) method.

Specified by:

canSetPosition in class ROI

setPosition5D

public void setPosition5D(Point5D position)

Description copied from class: ROI

Set the ROI position.
Note that not all ROI supports position modification and you should call ROI.canSetPosition() first to test if the operation is supported.

Specified by:

setPosition5D in class ROI

Parameters:

position - new ROI position

canTranslate

public boolean canTranslate()

Returns true if the ROI support translate operation.

See Also:

translate(double, double, double, double, double)

translate

public void translate(double dx,
             double dy,
             double dz,
             double dt,
             double dc)

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 canTranslate() first.

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:

canTranslate(), setPosition5D(Point5D)

contains

public boolean contains(ROI roi)

Description copied from class: ROI

Tests if the ROI entirely contains the specified ROI. WARNING: this method may be "pixel accurate" only depending the internal implementation.

Overrides:

contains in class ROI

Returns:

true if the current ROI entirely contains the specified ROI; false otherwise.

intersects

public boolean intersects(ROI roi)

Description copied from class: ROI

Tests if the current ROI intersects the specified ROI.
Note that this method may be "pixel accurate" only depending the internal implementation.

Overrides:

intersects in class ROI

Returns:

true if ROI intersect, false otherwise.

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 ROI

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.

getBooleanMask3D

public BooleanMask3D getBooleanMask3D(int z,
                             int t,
                             int c,
                             boolean inclusive)

Returns the BooleanMask3D object representing the XYZ volume content at specified Z, T, C position.
It contains the 3D rectangle mask bounds and the associated boolean array mask.

Parameters:

z - Z position we want to retrieve the boolean mask or -1 to retrieve the whole Z dimension

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.

getBooleanMask3D

public BooleanMask3D getBooleanMask3D(int t,
                             int c,
                             boolean inclusive)

Returns the BooleanMask3D object representing the XYZ volume content at specified T, C position.
It contains the 3D rectangle mask bounds and the associated boolean array mask.

Parameters:

inclusive - If true then all partially contained (intersected) pixels are included in the mask.

getBooleanMask4D

public BooleanMask4D getBooleanMask4D(int z,
                             int t,
                             int c,
                             boolean inclusive)

Returns the BooleanMask4D object representing the XYZT space content at specified Z and C position.

Parameters:

z - Z position we want to retrieve the boolean mask or -1 to retrieve the whole Z dimension

t - T position we want to retrieve the boolean mask or -1 to retrieve the whole T dimension

c - C position we want to retrieve the boolean mask.

inclusive - If true then all partially contained (intersected) pixels are included in the mask.

getBooleanMask4D

public BooleanMask4D getBooleanMask4D(int c,
                             boolean inclusive)

Get the BooleanMask4D object representing the roi for specified C position.
It contains the 4D rectangle mask bounds and the associated boolean array mask.

Parameters:

inclusive - If true then all partially contained (intersected) pixels are included in the mask.

getBooleanMask5D

public BooleanMask5D getBooleanMask5D(int z,
                             int t,
                             int c,
                             boolean inclusive)

Returns the BooleanMask5D object representing the XYZTC space content at specified Z, T, C position.

Parameters:

z - Z position we want to retrieve the boolean mask or -1 to retrieve the whole Z dimension

t - T position we want to retrieve the boolean mask or -1 to retrieve the whole T dimension

c - C position we want to retrieve the boolean mask or -1 to retrieve the whole C dimension

inclusive - If true then all partially contained (intersected) pixels are included in the mask.

getBooleanMask

public BooleanMask5D getBooleanMask(boolean inclusive)

Get the BooleanMask5D object representing the roi.
It contains the 5D rectangle mask bounds and the associated boolean array mask.

Parameters:

inclusive - If true then all partially contained (intersected) pixels are included in the mask.

computeNumberOfContourPoints

public double computeNumberOfContourPoints()

Description copied from class: ROI

Compute and returns the number of point (pixel) composing the ROI contour.

Specified by:

computeNumberOfContourPoints in class ROI

computeNumberOfPoints

public double computeNumberOfPoints()

Description copied from class: ROI

Compute and returns the number of point (pixel) contained in the ROI.

Specified by:

computeNumberOfPoints in class ROI