BooleanMask3D

java.lang.Object
- icy.roi.BooleanMask3D

All Implemented Interfaces:

java.lang.Cloneable
```
public class BooleanMask3D
extends java.lang.Object
implements java.lang.Cloneable
```
Class to define a 3D 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

Rectangle3D.Integer bounds
Region represented by the mask.

java.util.TreeMap<java.lang.Integer,BooleanMask2D> mask
Boolean mask 2D array.

Fields
Modifier and Type	Field and Description
`Rectangle3D.Integer`	`bounds` Region represented by the mask.
`java.util.TreeMap<java.lang.Integer,BooleanMask2D>`	`mask` Boolean mask 2D array.

Constructor Summary

Constructors
Constructor and Description
`BooleanMask3D()`
`BooleanMask3D(Point3D.Integer[] points)` Build a new 3D boolean mask from the specified array of `Point3D`.
`BooleanMask3D(Point3D[] points)` Build a new boolean mask from the specified array of `Point3D`.
`BooleanMask3D(Rectangle3D.Integer bounds, BooleanMask2D[] mask)` Build a new 3D boolean mask with specified bounds and 2D mask array.
`BooleanMask3D(Rectangle3D.Integer bounds, java.util.TreeMap<java.lang.Integer,BooleanMask2D> mask)`
`BooleanMask3D(java.util.TreeMap<java.lang.Integer,BooleanMask2D> mask)`

Method Summary

Methods
Modifier and Type	Method and Description
`java.lang.Object`	`clone()`
`boolean`	`contains(BooleanMask2D booleanMask, int z)` Return true if mask contains the specified 2D mask at position Z.
`boolean`	`contains(BooleanMask3D booleanMask)` Return true if mask contains the specified 3D mask.
`boolean`	`contains(int x, int y, int z)` Return true if mask contains the specified point
`BooleanMask3D`	`downscale()` Fast 2x down scaling (each 2x2x2 block points become 1 point).
`static BooleanMask3D`	`downscale(BooleanMask3D mask)` Fast 2x down scaling (each 2x2x2 block points become 1 point).
`static BooleanMask3D`	`downscale(BooleanMask3D mask, int nbPointForTrue)` Fast 2x down scaling (each 2x2x2 block points become 1 point).
`BooleanMask3D`	`downscale(int nbPointForTrue)` Fast 2x down scaling (each 2x2x2 block points become 1 point).
`BooleanMask3D`	`downscale2D()` Fast 2x down scaling (each 2x2 block points become 1 point).
`static BooleanMask3D`	`downscale2D(BooleanMask3D mask)` Fast 2x down scaling (each 2x2 block points become 1 point).
`static BooleanMask3D`	`downscale2D(BooleanMask3D mask, int nbPointForTrue)` Fast 2x down scaling (each 2x2 block points become 1 point).
`BooleanMask3D`	`downscale2D(int nbPointForTrue)` Fast 2x down scaling (each 2x2 block points become 1 point).
`double`	`getContourLength()` Computes and returns the length of the contour.
`Point3D.Integer[]`	`getContourPoints()` Return an array of `Point3D.Integer` containing the contour/surface points of the 3D mask.
`int[]`	`getContourPointsAsIntArray()` Return an array of integer containing the contour/surface points of the 3D mask.
`static BooleanMask3D`	`getExclusiveUnion(BooleanMask3D mask1, BooleanMask3D mask2)` Build resulting mask from exclusive union of the mask1 and mask2: mask1 xor mask2 = result ################ ################ ############## ############## ## ## ############ ############ #### #### ########## ########## ###### ###### ######## ######## ################ ###### ###### ###### ###### #### #### #### #### ## ## ## ##
`static BooleanMask3D`	`getIntersection(BooleanMask3D mask1, BooleanMask3D mask2)` Build resulting mask from intersection of the mask1 and mask2: mask1 intersect mask2 = result ################ ################ ################ ############## ############## ############ ############ ############ ######## ########## ########## #### ######## ######## ###### ###### #### #### ## ##
`BooleanMask2D`	`getMask2D(int z)` Returns the 2D boolean mask for the specified Z position
`int`	`getNumberOfPoints()` Return the number of points contained in this boolean mask.
`Rectangle3D.Integer`	`getOptimizedBounds()` Optimize mask bounds so it fits mask content.
`Rectangle3D.Integer`	`getOptimizedBounds(boolean compute2DBounds)` Optimize mask bounds so it fits mask content.
`Point3D.Integer[]`	`getPoints()` Return an array of `Point3D.Integer` representing all points of the current 3D mask.
`int[]`	`getPointsAsIntArray()` Return an array of integer representing all points of the current 3D mask.
`static BooleanMask3D`	`getSubtraction(BooleanMask3D mask1, BooleanMask3D mask2)` Build resulting mask from the subtraction of mask2 from mask1: mask1 - mask2 = result ################ ################ ############## ############## ## ############ ############ #### ########## ########## ###### ######## ######## ######## ###### ###### ###### #### #### #### ## ## ##
`static BooleanMask3D`	`getUnion(BooleanMask3D mask1, BooleanMask3D mask2)` Build resulting mask from union of the mask1 and mask2: mask1 + mask2 = result ################ ################ ################ ############## ############## ################ ############ ############ ################ ########## ########## ################ ######## ######## ################ ###### ###### ###### ###### #### #### #### #### ## ## ## ##
`boolean`	`intersects(BooleanMask2D booleanMask, int z)` Return true if mask intersects (contains at least one point) the specified 2D mask at position Z.
`boolean`	`intersects(BooleanMask3D booleanMask)` Return true if mask intersects (contains at least one point) the specified 3D mask region.
`boolean`	`isEmpty()` Return `true` if boolean mask is empty
`void`	`moveBounds(Rectangle3D.Integer value)` Change the bounds of BooleanMask.
`void`	`optimizeBounds()` Optimize mask bounds so it fits mask content.
`static int[]`	`toInt3D(int[] source2D, int z)` Transforms the specified 3D coordinates int array [x,y,z] in 4D coordinates int array [x,y,z,t] with the specified T value.
`BooleanMask3D`	`upscale()` Fast 2x up scaling (each point become 2x2x2 bloc point).
`static BooleanMask3D`	`upscale(BooleanMask3D mask)` Fast 2x up scaling (each point become 2x2x2 bloc points).
`BooleanMask3D`	`upscale2D()` Fast 2x up scaling (each point become 2x2 bloc point).
`static BooleanMask3D`	`upscale2D(BooleanMask3D mask)` Fast 2x up scaling (each point become 2x2 bloc points).

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

- Field Detail
  - bounds
```
public Rectangle3D.Integer bounds
```
    Region represented by the mask.
  - mask
```
public final java.util.TreeMap<java.lang.Integer,BooleanMask2D> mask
```
    Boolean mask 2D array.
- Constructor Detail
  - BooleanMask3D
```
public BooleanMask3D(Rectangle3D.Integer bounds,
             java.util.TreeMap<java.lang.Integer,BooleanMask2D> mask)
```
  - BooleanMask3D
```
public BooleanMask3D(java.util.TreeMap<java.lang.Integer,BooleanMask2D> mask)
```
  - BooleanMask3D
```
public BooleanMask3D(Rectangle3D.Integer bounds,
             BooleanMask2D[] mask)
```
    Build a new 3D boolean mask with specified bounds and 2D mask array.
    The 2D mask array length should be >= to bounds.getSizeZ().
  - BooleanMask3D
```
public BooleanMask3D(Point3D.Integer[] points)
```
    Build a new 3D boolean mask from the specified array of Point3D.
  - BooleanMask3D
```
public BooleanMask3D(Point3D[] points)
```
    Build a new boolean mask from the specified array of Point3D.
  - BooleanMask3D
```
public BooleanMask3D()
```
- Method Detail
  - getUnion
```
public static BooleanMask3D getUnion(BooleanMask3D mask1,
                     BooleanMask3D mask2)
```
    Build resulting mask from union of the mask1 and mask2:
```
        mask1          +       mask2        =      result
 
     ################     ################     ################
     ##############         ##############     ################
     ############             ############     ################
     ##########                 ##########     ################
     ########                     ########     ################
     ######                         ######     ######    ######
     ####                             ####     ####        ####
     ##                                 ##     ##            ##
 
```
  - getIntersection
```
public static BooleanMask3D getIntersection(BooleanMask3D mask1,
                            BooleanMask3D mask2)
```
    Build resulting mask from intersection of the mask1 and mask2:
```
        mask1     intersect     mask2      =        result
 
     ################     ################     ################
     ##############         ##############       ############
     ############             ############         ########
     ##########                 ##########           ####
     ########                     ########
     ######                         ######
     ####                             ####
     ##                                 ##
 
```
  - getExclusiveUnion
```
public static BooleanMask3D getExclusiveUnion(BooleanMask3D mask1,
                              BooleanMask3D mask2)
```
    Build resulting mask from exclusive union of the mask1 and mask2:
```
          mask1       xor      mask2        =       result
 
     ################     ################
     ##############         ##############     ##            ##
     ############             ############     ####        ####
     ##########                 ##########     ######    ######
     ########                     ########     ################
     ######                         ######     ######    ######
     ####                             ####     ####        ####
     ##                                 ##     ##            ##
 
```
  - getSubtraction
```
public static BooleanMask3D getSubtraction(BooleanMask3D mask1,
                           BooleanMask3D mask2)
```
    Build resulting mask from the subtraction of mask2 from mask1:
```
        mask1          -        mask2       =  result
 
     ################     ################
     ##############         ##############     ##
     ############             ############     ####
     ##########                 ##########     ######
     ########                     ########     ########
     ######                         ######     ######
     ####                             ####     ####
     ##                                 ##     ##
 
```
  - upscale
```
public static BooleanMask3D upscale(BooleanMask3D mask)
```
    Fast 2x up scaling (each point become 2x2x2 bloc points).
    This method create a new boolean mask.
  - downscale
```
public static BooleanMask3D downscale(BooleanMask3D mask,
                      int nbPointForTrue)
```
    Fast 2x down scaling (each 2x2x2 block points become 1 point).
    This method create a new boolean mask.
    
    Parameters:
    mask - the boolean mask to download
    nbPointForTrue - the minimum number of truepoints from a 2x2x2 block to give a true resulting point.
    Accepted value: 1 to 8 (default is 5)
  - downscale
```
public static BooleanMask3D downscale(BooleanMask3D mask)
```
    Fast 2x down scaling (each 2x2x2 block points become 1 point).
    This method create a new boolean mask.
  - upscale2D
```
public static BooleanMask3D upscale2D(BooleanMask3D mask)
```
    Fast 2x up scaling (each point become 2x2 bloc points).
    2D version (down scale is done on XY dimension only).
    This method create a new boolean mask.
  - downscale2D
```
public static BooleanMask3D downscale2D(BooleanMask3D mask,
                        int nbPointForTrue)
```
    Fast 2x down scaling (each 2x2 block points become 1 point).
    2D version (down scale is done on XY dimension only).
    This method create a new boolean mask.
    
    Parameters:
    mask - the boolean mask to download
    nbPointForTrue - the minimum number of truepoints from a 2x2 block to give a true resulting point.
    Accepted value: 1 to 4 (default is 3)
  - downscale2D
```
public static BooleanMask3D downscale2D(BooleanMask3D mask)
```
    Fast 2x down scaling (each 2x2 block points become 1 point).
    2D version (down scale is done on XY dimension only).
    This method create a new boolean mask.
  - getMask2D
```
public BooleanMask2D getMask2D(int z)
```
    Returns the 2D boolean mask for the specified Z position
  - isEmpty
```
public boolean isEmpty()
```
    Return true if boolean mask is empty
  - contains
```
public boolean contains(int x,
               int y,
               int z)
```
    Return true if mask contains the specified point
  - contains
```
public boolean contains(BooleanMask2D booleanMask,
               int z)
```
    Return true if mask contains the specified 2D mask at position Z.
  - contains
```
public boolean contains(BooleanMask3D booleanMask)
```
    Return true if mask contains the specified 3D mask.
  - intersects
```
public boolean intersects(BooleanMask2D booleanMask,
                 int z)
```
    Return true if mask intersects (contains at least one point) the specified 2D mask at position Z.
  - intersects
```
public boolean intersects(BooleanMask3D booleanMask)
```
    Return true if mask intersects (contains at least one point) the specified 3D mask region.
  - getOptimizedBounds
```
public Rectangle3D.Integer getOptimizedBounds(boolean compute2DBounds)
```
    Optimize mask bounds so it fits mask content.
  - getOptimizedBounds
```
public Rectangle3D.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(Rectangle3D.Integer value)
```
    Change the bounds of BooleanMask.
    Keep mask data intersecting from old bounds.
  - upscale
```
public BooleanMask3D upscale()
```
    Fast 2x up scaling (each point become 2x2x2 bloc point).
    This method create a new boolean mask.
  - downscale
```
public BooleanMask3D downscale(int nbPointForTrue)
```
    Fast 2x down scaling (each 2x2x2 block points become 1 point).
    This method create a new boolean mask.
    
    Parameters:
    nbPointForTrue - the minimum number of truepoints from a 2x2x2 block to give a true resulting point.
    Accepted value: 1-8 (default is 5).
  - downscale
```
public BooleanMask3D downscale()
```
    Fast 2x down scaling (each 2x2x2 block points become 1 point).
    This method create a new boolean mask.
  - upscale2D
```
public BooleanMask3D upscale2D()
```
    Fast 2x up scaling (each point become 2x2 bloc point).
    2D version (down scale is done on XY dimension only).
    This method create a new boolean mask.
  - downscale2D
```
public BooleanMask3D downscale2D(int nbPointForTrue)
```
    Fast 2x down scaling (each 2x2 block points become 1 point).
    2D version (down scale is done on XY dimension only).
    This method create a new boolean mask.
    
    Parameters:
    nbPointForTrue - the minimum number of truepoints from a 2x2 block to give a true resulting point.
    Accepted value: 1-4 (default is 3).
  - downscale2D
```
public BooleanMask3D downscale2D()
```
    Fast 2x down scaling (each 2x2 block points become 1 point).
    2D version (down scale is done on XY dimension only).
    This method create a new boolean mask.
  - toInt3D
```
public static int[] toInt3D(int[] source2D,
            int z)
```
    Transforms the specified 3D coordinates int array [x,y,z] in 4D coordinates int array [x,y,z,t] with the specified T value.
  - getNumberOfPoints
```
public int getNumberOfPoints()
```
    Return the number of points contained in this boolean mask.
  - getPoints
```
public Point3D.Integer[] getPoints()
```
    Return an array of Point3D.Integer representing all points of the current 3D mask.
    Points are returned in ascending XYZ order.
  - getPointsAsIntArray
```
public int[] getPointsAsIntArray()
```
    Return an array of integer representing all points of the current 3D mask.
    result.length = number of point * 3
    result[(pt * 3) + 0] = X coordinate for point pt.
    result[(pt * 3) + 1] = Y coordinate for point pt.
    result[(pt * 3) + 2] = Z coordinate for point pt.
    Points are returned in ascending XYZ order.
  - getContourPoints
```
public Point3D.Integer[] getContourPoints()
```
    Return an array of Point3D.Integer containing the contour/surface points of the 3D mask.
    Points are returned in ascending XYZ order.
    
    WARNING: The default implementation is not totally accurate.
    It returns all points from the first and the last Z slices + contour points for intermediate Z slices.
    
    See Also:
    getContourPointsAsIntArray()
  - getContourPointsAsIntArray
```
public int[] getContourPointsAsIntArray()
```
    Return an array of integer containing the contour/surface points of the 3D mask.
    result.length = number of point * 3
    result[(pt * 3) + 0] = X coordinate for point pt.
    result[(pt * 3) + 1] = Y coordinate for point pt.
    result[(pt * 3) + 2] = Z coordinate for point pt.
    Points are returned in ascending XYZ order.
    
    WARNING: The default implementation is not totally accurate.
    It returns all points from the first and the last Z slices + contour points for intermediate Z slices.
    
    See Also:
    getContourPoints()
  - getContourLength
```
public double getContourLength()
```
    Computes and returns the length of the contour.
    This is different from the number of contour point as it takes care of approximating correctly distance between each contour point.
    
    Returns:
    the length of the contour
  - clone
```
public java.lang.Object clone()
```
    Overrides:
    
    clone in class java.lang.Object

Class BooleanMask3D

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

bounds

mask

Constructor Detail

BooleanMask3D

BooleanMask3D

BooleanMask3D

BooleanMask3D

BooleanMask3D

BooleanMask3D

Method Detail

getUnion

getIntersection

getExclusiveUnion

getSubtraction

upscale

downscale

downscale

upscale2D

downscale2D

downscale2D

getMask2D

isEmpty

contains

contains

contains

intersects

intersects

getOptimizedBounds

getOptimizedBounds

optimizeBounds

moveBounds

upscale

downscale

downscale

upscale2D

downscale2D

downscale2D

toInt3D

getNumberOfPoints

getPoints

getPointsAsIntArray

getContourPoints

getContourPointsAsIntArray

getContourLength

clone