icy.roi

Class BooleanMask5D

java.lang.Object

icy.roi.BooleanMask5D

public class BooleanMask5D
extends java.lang.Object

Class to define a 5D boolean mask region and make basic boolean operation between masks.
The bounds property of this object represents the region defined by the boolean mask.

Author:

Stephane

Field Summary

Fields

Modifier and Type	Field and Description
Rectangle5D.Integer	bounds Region represented by the mask.
java.util.TreeMap<java.lang.Integer,BooleanMask4D>	mask Boolean mask 4D array.

Constructor Summary

Constructors

Constructor and Description
BooleanMask5D()
BooleanMask5D(Point5D.Integer[] points) Build a new 4D boolean mask from the specified array of Point5D.
BooleanMask5D(Point5D[] points) Build a new boolean mask from the specified array of Point5D.
BooleanMask5D(Rectangle5D.Integer bounds, BooleanMask4D[] mask) Build a new 4D boolean mask with specified bounds and 4D mask array.

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.Object	clone()
boolean	contains(BooleanMask2D booleanMask, int z, int t, int c) Return true if mask contains the specified 2D mask at position Z, T, C
boolean	contains(BooleanMask3D booleanMask, int t, int c) Return true if mask contains the specified 3D mask at position T, C
boolean	contains(BooleanMask4D booleanMask, int c) Return true if mask contains the specified 4D mask at position C
boolean	contains(BooleanMask5D booleanMask) Return true if mask contains the specified 5D mask.
boolean	contains(int x, int y, int z, int t, int c) Return true if mask contains the specified point
Point5D.Integer[]	getContourPoints() Return an array of Point5D.Integer containing the contour/surface points of the 5D mask.
int[]	getContourPointsAsIntArray() Return an array of integer containing the contour/surface points of the 5D mask.
static BooleanMask5D	getExclusiveUnion(BooleanMask5D mask1, BooleanMask5D mask2) Build resulting mask from exclusive union of the mask1 and mask2: mask1 xor mask2 = result ################ ################ ############## ############## ## ## ############ ############ #### #### ########## ########## ###### ###### ######## ######## ################ ###### ###### ###### ###### #### #### #### #### ## ## ## ##
static BooleanMask5D	getIntersection(BooleanMask5D mask1, BooleanMask5D mask2) Build resulting mask from intersection of the mask1 and mask2: mask1 intersect mask2 = result ################ ################ ################ ############## ############## ############ ############ ############ ######## ########## ########## #### ######## ######## ###### ###### #### #### ## ##
BooleanMask2D	getMask2D(int z, int t, int c) Returns the 2D boolean mask for the specified Z, T, C position
BooleanMask3D	getMask3D(int t, int c) Returns the 3D boolean mask for the specified T, C position
BooleanMask4D	getMask4D(int c) Returns the 4D boolean mask for the specified C position
int	getNumberOfPoints() Return the number of points contained in this boolean mask.
Rectangle5D.Integer	getOptimizedBounds() Optimize mask bounds so it fits mask content.
Rectangle5D.Integer	getOptimizedBounds(boolean compute4DBounds) Optimize mask bounds so it fits mask content.
Point5D.Integer[]	getPoints() Return an array of Point5D.Integer representing all points of the current 5D mask.
int[]	getPointsAsIntArray() Return an array of integer representing all points of the current 5D mask.
static BooleanMask5D	getSubtraction(BooleanMask5D mask1, BooleanMask5D mask2) Build resulting mask from the subtraction of mask2 from mask1: mask1 - mask2 = result ################ ################ ############## ############## ## ############ ############ #### ########## ########## ###### ######## ######## ######## ###### ###### ###### #### #### #### ## ## ##
static BooleanMask5D	getUnion(BooleanMask5D mask1, BooleanMask5D mask2) Build resulting mask from union of the mask1 and mask2: mask1 + mask2 = result ################ ################ ################ ############## ############## ################ ############ ############ ################ ########## ########## ################ ######## ######## ################ ###### ###### ###### ###### #### #### #### #### ## ## ## ##
boolean	intersects(BooleanMask2D booleanMask, int z, int t, int c) Return true if mask intersects (contains at least one point) the specified 2D mask at position Z, T, C
boolean	intersects(BooleanMask3D booleanMask, int t, int c) Return true if mask intersects (contains at least one point) the specified 3D mask at position T, C
boolean	intersects(BooleanMask4D booleanMask, int c) Return true if mask intersects (contains at least one point) the specified 4D mask at position C
boolean	intersects(BooleanMask5D booleanMask) Return true if mask intersects (contains at least one point) the specified 5D mask region
boolean	isEmpty() Return true if boolean mask is empty
void	moveBounds(Rectangle5D.Integer value) Change the bounds of BooleanMask.
void	optimizeBounds() Optimize mask bounds so it fits mask content.
static int[]	toInt5D(int[] source4D, int c) Transforms the specified 4D coordinates int array [x,y,z,t] in 5D coordinates int array [x,y,z,t,c] with the specified C value.

Methods inherited from class java.lang.Object

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

Field Detail

bounds

public Rectangle5D.Integer bounds

Region represented by the mask.

mask

public final java.util.TreeMap<java.lang.Integer,BooleanMask4D> mask

Boolean mask 4D array.

Constructor Detail

BooleanMask5D

public BooleanMask5D(Rectangle5D.Integer bounds,
             BooleanMask4D[] mask)

Build a new 4D boolean mask with specified bounds and 4D mask array.
The 4D mask array length should be >= to bounds.getSizeT().

BooleanMask5D

public BooleanMask5D(Point5D.Integer[] points)

Build a new 4D boolean mask from the specified array of Point5D.

BooleanMask5D

public BooleanMask5D(Point5D[] points)

Build a new boolean mask from the specified array of Point5D.

BooleanMask5D

public BooleanMask5D()

Method Detail

getUnion

public static BooleanMask5D getUnion(BooleanMask5D mask1,
                     BooleanMask5D mask2)

Build resulting mask from union of the mask1 and mask2:

        mask1          +       mask2        =      result
 
     ################     ################     ################
     ##############         ##############     ################
     ############             ############     ################
     ##########                 ##########     ################
     ########                     ########     ################
     ######                         ######     ######    ######
     ####                             ####     ####        ####
     ##                                 ##     ##            ##
 

getIntersection

public static BooleanMask5D getIntersection(BooleanMask5D mask1,
                            BooleanMask5D mask2)

Build resulting mask from intersection of the mask1 and mask2:

        mask1     intersect     mask2      =        result
 
     ################     ################     ################
     ##############         ##############       ############
     ############             ############         ########
     ##########                 ##########           ####
     ########                     ########
     ######                         ######
     ####                             ####
     ##                                 ##
 

getExclusiveUnion

public static BooleanMask5D getExclusiveUnion(BooleanMask5D mask1,
                              BooleanMask5D mask2)

Build resulting mask from exclusive union of the mask1 and mask2:

          mask1       xor      mask2        =       result
 
     ################     ################
     ##############         ##############     ##            ##
     ############             ############     ####        ####
     ##########                 ##########     ######    ######
     ########                     ########     ################
     ######                         ######     ######    ######
     ####                             ####     ####        ####
     ##                                 ##     ##            ##
 

getSubtraction

public static BooleanMask5D getSubtraction(BooleanMask5D mask1,
                           BooleanMask5D mask2)

Build resulting mask from the subtraction of mask2 from mask1:

        mask1          -        mask2       =  result
 
     ################     ################
     ##############         ##############     ##
     ############             ############     ####
     ##########                 ##########     ######
     ########                     ########     ########
     ######                         ######     ######
     ####                             ####     ####
     ##                                 ##     ##
 

getMask4D

public BooleanMask4D getMask4D(int c)

Returns the 4D boolean mask for the specified C position

getMask3D

public BooleanMask3D getMask3D(int t,
                      int c)

Returns the 3D boolean mask for the specified T, C position

getMask2D

public BooleanMask2D getMask2D(int z,
                      int t,
                      int c)

Returns the 2D boolean mask for the specified Z, T, C position

isEmpty

public boolean isEmpty()

Return true if boolean mask is empty

contains

public boolean contains(int x,
               int y,
               int z,
               int t,
               int c)

Return true if mask contains the specified point

contains

public boolean contains(BooleanMask2D booleanMask,
               int z,
               int t,
               int c)

Return true if mask contains the specified 2D mask at position Z, T, C

contains

public boolean contains(BooleanMask3D booleanMask,
               int t,
               int c)

Return true if mask contains the specified 3D mask at position T, C

contains

public boolean contains(BooleanMask4D booleanMask,
               int c)

Return true if mask contains the specified 4D mask at position C

contains

public boolean contains(BooleanMask5D booleanMask)

Return true if mask contains the specified 5D mask.

intersects

public boolean intersects(BooleanMask2D booleanMask,
                 int z,
                 int t,
                 int c)

Return true if mask intersects (contains at least one point) the specified 2D mask at position Z, T, C

intersects

public boolean intersects(BooleanMask3D booleanMask,
                 int t,
                 int c)

Return true if mask intersects (contains at least one point) the specified 3D mask at position T, C

intersects

public boolean intersects(BooleanMask4D booleanMask,
                 int c)

Return true if mask intersects (contains at least one point) the specified 4D mask at position C

intersects

public boolean intersects(BooleanMask5D booleanMask)

Return true if mask intersects (contains at least one point) the specified 5D mask region

getOptimizedBounds

public Rectangle5D.Integer getOptimizedBounds(boolean compute4DBounds)

Optimize mask bounds so it fits mask content.

getOptimizedBounds

public Rectangle5D.Integer getOptimizedBounds()

Optimize mask bounds so it fits mask content.

optimizeBounds

public void optimizeBounds()

Optimize mask bounds so it fits mask content.

moveBounds

public void moveBounds(Rectangle5D.Integer value)

Change the bounds of BooleanMask.
Keep mask data intersecting from old bounds.

toInt5D

public static int[] toInt5D(int[] source4D,
            int c)

Transforms the specified 4D coordinates int array [x,y,z,t] in 5D coordinates int array [x,y,z,t,c] with the specified C value.

getContourPoints

public Point5D.Integer[] getContourPoints()

Return an array of Point5D.Integer containing the contour/surface points of the 5D mask.
Points are returned in ascending XYZTC order.

WARNING: The basic implementation is not totally accurate.
It returns all points from the first and the last C slices + contour points for intermediate C slices.

See Also:

getContourPointsAsIntArray()

getContourPointsAsIntArray

public int[] getContourPointsAsIntArray()

Return an array of integer containing the contour/surface points of the 5D mask.
result.length = number of point * 4
result[(pt * 4) + 0] = X coordinate for point pt.
result[(pt * 4) + 1] = Y coordinate for point pt.
result[(pt * 4) + 2] = Z coordinate for point pt.
result[(pt * 4) + 3] = T coordinate for point pt.
result[(pt * 5) + 4] = C coordinate for point pt.
Points are returned in ascending XYZTC order.

WARNING: The basic implementation is not totally accurate.
It returns all points from the first and the last C slices + contour points for intermediate C slices.

See Also:

getContourPoints()

getNumberOfPoints

public int getNumberOfPoints()

Return the number of points contained in this boolean mask.

getPoints

public Point5D.Integer[] getPoints()

Return an array of Point5D.Integer representing all points of the current 5D mask.
Points are returned in ascending XYZTC order.

getPointsAsIntArray

public int[] getPointsAsIntArray()

Return an array of integer representing all points of the current 5D mask.
result.length = number of point * 5
result[(pt * 5) + 0] = X coordinate for point pt.
result[(pt * 5) + 1] = Y coordinate for point pt.
result[(pt * 5) + 2] = Z coordinate for point pt.
result[(pt * 5) + 3] = T coordinate for point pt.
result[(pt * 5) + 4] = C coordinate for point pt.
Points are returned in ascending XYZTC order.

clone

public java.lang.Object clone()

Overrides:

clone in class java.lang.Object