icy.roi

Class ROI4D

java.lang.Object

icy.roi.ROI

icy.roi.ROI4D

All Implemented Interfaces:

ChangeListener, XMLPersistent

Direct Known Subclasses:

ROI4DStack

public abstract class ROI4D
extends ROI

4D 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

Modifier and Type	Field and Description
static java.lang.String	ID_C

Fields inherited from class icy.roi.ROI

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

Constructor Summary

Constructors

Constructor and Description
ROI4D()

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.
abstract Rectangle4D	computeBounds4D() Calculate and returns the 4D bounding box of the ROI.
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.
abstract boolean	contains(double x, double y, double z, double t) Tests if the specified coordinates are inside the ROI.
boolean	contains(double x, double y, double z, double t, double c) Tests if a specified 5D point is inside the ROI.
abstract boolean	contains(double x, double y, double z, double t, double sizeX, double sizeY, double sizeZ, double sizeT) Tests if the ROI entirely contains the specified 4D rectangular area.
boolean	contains(double x, double y, double z, double t, double c, double sizeX, double sizeY, double sizeT, double sizeZ, double sizeC) Tests if the ROI entirely contains the specified 5D rectangular area.
boolean	contains(Point4D p) Tests if a specified Point4D is inside the ROI.
boolean	contains(Rectangle4D r) Tests if the interior of the ROI entirely contains the specified Rectangle4D.
boolean	contains(ROI roi) Tests if the ROI entirely contains the specified ROI.
BooleanMask4D	getBooleanMask(boolean inclusive) Get the BooleanMask4D object representing the roi.
BooleanMask2D	getBooleanMask2D(int z, int t, boolean inclusive) Get the BooleanMask2D object representing the roi for the specified Z,T position.
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, boolean inclusive) Get the boolean bitmap mask for the specified rectangular area of the roi and for the specified Z,T 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, boolean inclusive) Get the boolean bitmap mask for the specified rectangular area of the roi and for the specified Z,T position.
BooleanMask3D	getBooleanMask3D(int t, boolean inclusive) Get the BooleanMask3D object representing the roi for specified T 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 z, int t, int c, boolean inclusive) Returns the BooleanMask4D object representing the XYZT space content at specified Z, T, C position.
Rectangle4D.Integer	getBounds() Returns an integer Rectangle4D that completely encloses the ROI.
Rectangle4D	getBounds4D() Returns the bounding box of the ROI.
int	getC() Returns the C position.
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
Point4D.Integer	getPosition() Returns the integer ROI position which normally correspond to the minimum point of the ROI bounds.
Point4D	getPosition4D() Returns the ROI position which normally correspond to the minimum point of the ROI bounds.
static java.util.ArrayList<ROI4D>	getROI4DList(java.util.ArrayList<ROI> rois) Deprecated. Use getROI4DList(List) instead.
static java.util.List<ROI4D>	getROI4DList(java.util.List<ROI> rois) Return all 4D ROI from the ROI list
abstract boolean	intersects(double x, double y, double z, double t, double sizeX, double sizeY, double sizeZ, double sizeT) Tests if the interior of the ROI intersects the interior of a specified 4D rectangular area.
boolean	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(Rectangle4D r) Tests if the interior of the ROI intersects the interior of a specified Rectangle4D.
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.
boolean	isActiveFor(int c) Return true if the ROI is active for the specified C coordinate
boolean	loadFromXML(org.w3c.dom.Node node) LOAD
boolean	saveToXML(org.w3c.dom.Node node) SAVE
void	setBounds4D(Rectangle4D bounds) Set the ROI 4D bounds.
void	setBounds5D(Rectangle5D bounds) Set the ROI bounds.
void	setC(int value) Sets C position of this 4D ROI.
void	setPosition4D(Point4D position) Set the ROI 4D position.
void	setPosition5D(Point5D position) Set the ROI position.
void	translate(double dx, double dy, double dz, double dt) 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, 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, hasSelectedPoint, internalFocus, internalSelect, internalUnfocus, internalUnselect, intersect, intersects, isAttached, isCreating, isDefaultName, isEditable, isEmpty, isFocused, isReadOnly, isSelected, isUpdating, loadFromXML, loadROIsFromXML, merge, mergeWith, nameChanged, onChanged, painterChanged, propertyChanged, remove, remove, removeListener, roiChanged, roiChanged, roiChanged, saveROIsToXML, 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

Field Detail

ID_C

public static final java.lang.String ID_C

See Also:

Constant Field Values

Constructor Detail

ROI4D

public ROI4D()

Method Detail

getROI4DList

@Deprecated
public static java.util.ArrayList<ROI4D> getROI4DList(java.util.ArrayList<ROI> rois)

Deprecated. Use getROI4DList(List) instead.

getROI4DList

public static java.util.List<ROI4D> getROI4DList(java.util.List<ROI> rois)

Return all 4D 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

contains

public boolean contains(Point4D p)

Tests if a specified Point4D is inside the ROI.

Parameters:

p - the specified Point4D to be tested

Returns:

true if the specified Point3D is inside the boundary of the ROI; false otherwise.

contains

public boolean contains(Rectangle4D r)

Tests if the interior of the ROI entirely contains the specified Rectangle4D. 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 Rectangle3D are prohibitively expensive.

This means that for some ROIs this method might return false even though the ROI contains the Rectangle4D.

Parameters:

r - The specified Rectangle4D

Returns:

true if the interior of the ROI entirely contains the Rectangle4D; false otherwise or, if the ROI contains the Rectangle4D 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)

contains

public abstract boolean contains(double x,
               double y,
               double z,
               double t)

Tests if the specified coordinates are inside the ROI.

Parameters:

x - the specified X coordinate to be tested

y - the specified Y coordinate to be tested

z - the specified Z coordinate to be tested

t - the specified T coordinate to be tested

Returns:

true if the specified 4D coordinates are inside the ROI boundary; false otherwise.

contains

public abstract boolean contains(double x,
               double y,
               double z,
               double t,
               double sizeX,
               double sizeY,
               double sizeZ,
               double sizeT)

Tests if the ROI entirely contains the specified 4D rectangular area. 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 minimum corner position of the specified rectangular area

y - the Y coordinate of the minimum corner position of the specified rectangular area

z - the Z coordinate of the minimum corner position of the specified rectangular area

t - the T coordinate of the minimum corner position of the specified rectangular area

sizeX - size for X dimension of the specified rectangular area

sizeY - size for Y dimension of the specified rectangular area

sizeZ - size for Z dimension of the specified rectangular area

sizeT - size for T dimension of the specified rectangular area

Returns:

true if the interior of the ROI entirely contains the specified 4D rectangular area; false otherwise or, if the ROI contains the 4D rectangular area and the intersects method returns true and the containment calculations would be too expensive to perform.

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 sizeT,
               double sizeZ,
               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

sizeT - the Z size of the specified rectangular area

sizeZ - 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(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(Rectangle4D r)

Tests if the interior of the ROI intersects the interior of a specified Rectangle4D. The ROI.intersects() method allows a ROI implementation to conservatively return true when:

• there is a high probability that the Rectangle4D 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 Rectangle4D does not intersect the ROI.

Parameters:

r - the specified Rectangle4D

Returns:

true if the interior of the ROI and the interior of the specified Rectangle4D intersect, or are both highly likely to intersect and intersection calculations would be too expensive to perform; false otherwise.

See Also:

intersects(double, double, double,double, double, double, double, double)

intersects

public abstract boolean intersects(double x,
                 double y,
                 double z,
                 double t,
                 double sizeX,
                 double sizeY,
                 double sizeZ,
                 double sizeT)

Tests if the interior of the ROI intersects the interior of a specified 4D rectangular area. The 4D rectangular area is considered to intersect the ROI if any point is contained in both the interior of the ROI and the specified rectangular area.

The ROI.intersects() method allows a ROI implementation to conservatively return true when:

• there is a high probability that the 4D rectangular area and the ROI intersect, but
• the calculations to accurately determine this intersection are prohibitively expensive.

This means that for some ROIs this method might return true even though the 4D rectangular area does not intersect the ROI.

Parameters:

x - the X coordinate of the minimum corner position of the specified rectangular area

y - the Y coordinate of the minimum corner position of the specified rectangular area

z - the Z coordinate of the minimum corner position of the specified rectangular area

t - the T coordinate of the minimum corner position of the specified rectangular area

sizeX - size for X dimension of the specified rectangular area

sizeY - size for Y dimension of the specified rectangular area

sizeZ - size for Z dimension of the specified rectangular area

sizeT - size for T dimension of the specified rectangular area

Returns:

true if the interior of the ROI and the interior of the rectangular area intersect, or are both highly likely to intersect and intersection calculations would be too expensive to perform; false otherwise.

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.

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.

computeBounds4D

public abstract Rectangle4D computeBounds4D()

Calculate and returns the 4D bounding box of the ROI.
This method is used by getBounds4D() which should try to cache the result as the bounding box calculation can take some computation time for complex ROI.

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

getBounds

public Rectangle4D.Integer getBounds()

Returns an integer Rectangle4D that completely encloses the ROI. Note that there is no guarantee that the returned Rectangle4D is the smallest bounding box that encloses the ROI, only that the ROI lies entirely within the indicated Rectangle4D. The returned Rectangle4D might also fail to completely enclose the ROI if the ROI overflows the limited range of the integer data type. The getBounds4D method generally returns a tighter bounding box due to its greater flexibility in representation.

Returns:

an integer Rectangle4D that completely encloses the ROI.

getBounds4D

public Rectangle4D getBounds4D()

Returns the bounding box of the ROI. Note that there is no guarantee that the returned Rectangle4D is the smallest bounding box that encloses the ROI, only that the ROI lies entirely within the indicated Rectangle4D.

Returns:

an instance of Rectangle4D that is a bounding box of the ROI.

getPosition

public Point4D.Integer getPosition()

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

See Also:

getBounds()

getPosition4D

public Point4D getPosition4D()

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

See Also:

getBounds4D()

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

setBounds4D

public void setBounds4D(Rectangle4D bounds)

Set the ROI 4D 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 4D bounds

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

setPosition4D

public void setPosition4D(Point4D position)

Set the ROI 4D 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 4D position

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)

translate

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

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

See Also:

canTranslate(), setPosition4D(Point4D)

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 boolean[] getBooleanMask2D(int x,
                         int y,
                         int width,
                         int height,
                         int z,
                         int t,
                         boolean inclusive)

Get the boolean bitmap mask for the specified rectangular area of the roi and for the specified Z,T position.
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] =

Parameters:

x - the X coordinate of the upper-left corner of the specified rectangular area

y - the Y coordinate of the upper-left corner of the specified rectangular area

width - the width of the specified rectangular area

height - the height of the specified rectangular area

z - Z position we want to retrieve the boolean mask

t - T position we want to retrieve the boolean mask

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

Returns:

the boolean bitmap mask

getBooleanMask2D

public boolean[] getBooleanMask2D(java.awt.Rectangle rect,
                         int z,
                         int t,
                         boolean inclusive)

Get the boolean bitmap mask for the specified rectangular area of the roi and for the specified Z,T position.
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

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)

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.

getBooleanMask2D

public BooleanMask2D getBooleanMask2D(int z,
                             int t,
                             boolean inclusive)

Get the BooleanMask2D object representing the roi for the specified Z,T position.
It contains the rectangle mask bounds and the associated boolean array mask.
if the pixel (x,y) is contained in the roi Z,T position then result.mask[(y * w) + x] = true
if the pixel (x,y) is not contained in the roi Z,T position then result.mask[(y * w) + x] = false

Parameters:

z - Z position we want to retrieve the boolean mask

t - T position we want to retrieve the boolean mask

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

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.
Set it to -1 to retrieve the mask whatever is the C position of this ROI4D.

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

getBooleanMask3D

public BooleanMask3D getBooleanMask3D(int t,
                             boolean inclusive)

Get the BooleanMask3D object representing the roi for specified T 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, 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.
Set it to -1 to retrieve the mask whatever is the C position of this ROI4D.

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

getBooleanMask

public BooleanMask4D getBooleanMask(boolean inclusive)

Get the BooleanMask4D object representing the roi.
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.

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

getC

public int getC()

Returns the C position.
-1 is a special value meaning the ROI is set on all C channels (infinite C dimension).

setC

public void setC(int value)

Sets C position of this 4D ROI.
You cannot set the ROI on a negative C position as -1 is a special value meaning the ROI is set on all C channels (infinite C dimension).

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

isActiveFor

public boolean isActiveFor(int c)

Return true if the ROI is active for the specified C coordinate

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