QuickEllipsoid (BoneJ Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.bonej.ops.ellipsoid.QuickEllipsoid

```
public class QuickEllipsoid
extends Object
```
Represents an ellipsoid defined by its centroid, eigenvalues and 3x3 eigenvector matrix. Semiaxis lengths (radii) are calculated as the inverse square root of the eigenvalues.

Author:

Michael Doube, Alessandro Felder

Constructor Summary

Constructors
Constructor and Description
`QuickEllipsoid(double[] radii, double[] centroid, double[][] eigenVectors)` Construct an QuickEllipsoid from the radii (a,b,c), centroid (cx, cy, cz) and Eigenvectors.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`contains(double x, double y, double z)` Method based on the inequality (X-X0)^T H (X-X0) ≤ 1 Where X is the test point, X0 is the centroid, H is the ellipsoid's 3x3 matrix
`void`	`contract(double increment)` Constrict all three axes by a fractional increment
`QuickEllipsoid`	`copy()` Perform a deep copy of this QuickEllipsoid
`void`	`dilate(double da, double db, double dc)` Dilate the ellipsoid semiaxes by independent absolute amounts
`double[][]`	`getAxisAlignRandomlyDistributedSurfacePoints(int n)`
`double[]`	`getCentre()`
`double[]`	`getRadii()` Gets a copy of the radii.
`double[][]`	`getRotation()` Return a copy of the ellipsoid's eigenvector matrix
`double[]`	`getSortedRadii()` Get the radii sorted in ascending order.
`double[][]`	`getSurfacePoints(double[][] vectors)`
`double`	`getVolume()` Gets the volume of this ellipsoid, calculated as PI * a * b * c * 4 / 3
`void`	`rotate(double[][] rotation)` Rotate the ellipsoid by the given 3x3 Matrix
`void`	`setCentroid(double x, double y, double z)` Translate the ellipsoid to a given new centroid
`void`	`setRotation(double[][] rotation)` Set rotation to the supplied rotation matrix.
`static double[][]`	`transpose(double[][] a)` Transpose a 3x3 matrix in double[][] format.

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

- Constructor Detail
  - QuickEllipsoid
```
public QuickEllipsoid(double[] radii,
                      double[] centroid,
                      double[][] eigenVectors)
```
    Construct an QuickEllipsoid from the radii (a,b,c), centroid (cx, cy, cz) and Eigenvectors.
    
    Parameters:
    
    radii - radii (a,b,c) as a double array
    
    centroid - ellipsoid centre x,y,z coordinates as a double array
    
    eigenVectors - the orientation of the ellipsoid.
- Method Detail
  - transpose
```
public static double[][] transpose(double[][] a)
```
    Transpose a 3x3 matrix in double[][] format. Does no error checking.
    
    Parameters:
    
    a - a matrix.
    
    Returns:
    
    new transposed matrix.
  - contains
```
public boolean contains(double x,
                        double y,
                        double z)
```
    Method based on the inequality (X-X0)^T H (X-X0) ≤ 1 Where X is the test point, X0 is the centroid, H is the ellipsoid's 3x3 matrix
    
    Parameters:
    
    x - x-coordinate of the point.
    
    y - y-coordinate of the point.
    
    z - z-coordinate of the point.
    
    Returns:
    
    true if the point (x,y,z) lies inside or on the ellipsoid, false otherwise
  - contract
```
public void contract(double increment)
```
    Constrict all three axes by a fractional increment
    
    Parameters:
    
    increment - scaling factor.
  - copy
```
public QuickEllipsoid copy()
```
    Perform a deep copy of this QuickEllipsoid
    
    Returns:
    
    a copy of the instance.
  - dilate
```
public void dilate(double da,
                   double db,
                   double dc)
            throws IllegalArgumentException
```
    Dilate the ellipsoid semiaxes by independent absolute amounts
    
    Parameters:
    
    da - value added to the 1st radius.
    
    db - value added to the 2nd radius.
    
    dc - value added to the 3rd radius.
    
    Throws:
    
    IllegalArgumentException - if new semi-axes are non-positive.
  - getCentre
```
public double[] getCentre()
```
  - getRadii
```
public double[] getRadii()
```
    Gets a copy of the radii.
    
    Returns:
    
    the semiaxis lengths a, b and c. Note these are not ordered by size, but the order does relate to the 0th, 1st and 2nd columns of the rotation matrix respectively.
  - getRotation
```
public double[][] getRotation()
```
    Return a copy of the ellipsoid's eigenvector matrix
    
    Returns:
    
    a 3x3 rotation matrix
  - setRotation
```
public void setRotation(double[][] rotation)
```
    Set rotation to the supplied rotation matrix. Does no error checking.
    
    Parameters:
    
    rotation - a 3x3 rotation matrix
  - getSortedRadii
```
public double[] getSortedRadii()
```
    Get the radii sorted in ascending order. Note that there is no guarantee that this ordering relates at all to the eigenvectors or eigenvalues.
    
    Returns:
    
    radii in ascending order
  - getSurfacePoints
```
public double[][] getSurfacePoints(double[][] vectors)
```
  - getAxisAlignRandomlyDistributedSurfacePoints
```
public double[][] getAxisAlignRandomlyDistributedSurfacePoints(int n)
```
  - getVolume
```
public double getVolume()
```
    Gets the volume of this ellipsoid, calculated as PI * a * b * c * 4 / 3
    
    Returns:
    
    copy of the stored volume value.
  - rotate
```
public void rotate(double[][] rotation)
```
    Rotate the ellipsoid by the given 3x3 Matrix
    
    Parameters:
    
    rotation - a 3x3 rotation matrix
  - setCentroid
```
public void setCentroid(double x,
                        double y,
                        double z)
```
    Translate the ellipsoid to a given new centroid
    
    Parameters:
    
    x - new centroid x-coordinate
    
    y - new centroid y-coordinate
    
    z - new centroid z-coordinate

Class QuickEllipsoid

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

QuickEllipsoid

Method Detail

transpose

contains

contract

copy

dilate

getCentre

getRadii

getRotation

setRotation

getSortedRadii

getSurfacePoints

getAxisAlignRandomlyDistributedSurfacePoints

getVolume

rotate

setCentroid