SimilarityModel3D (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.models.AbstractModel<M>
- - mpicbg.models.AbstractAffineModel3D<SimilarityModel3D>
  - - bdv.viewer.animate.SimilarityModel3D

All Implemented Interfaces:

Serializable, Affine3D<SimilarityModel3D>, Boundable, CoordinateTransform, InverseBoundable, InverseCoordinateTransform, InvertibleBoundable, InvertibleCoordinateTransform, Model<SimilarityModel3D>
```
public class SimilarityModel3D
extends AbstractAffineModel3D<SimilarityModel3D>
implements InvertibleBoundable
```
3d-rigid transformation models to be applied to points in 3d-space. This function uses the method by Horn, using quaternions: Closed-form solution of absolute orientation using unit quaternions, Horn, B. K. P., Journal of the Optical Society of America A, Vol. 4, page 629, April 1987

Version:

0.1b

Author:

John Bogovic, Johannes Schindelin (quaternion logic and implementation), Stephan Preibisch

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`protected double`	`i00`
`protected double`	`i01`
`protected double`	`i02`
`protected double`	`i03`
`protected double`	`i10`
`protected double`	`i11`
`protected double`	`i12`
`protected double`	`i13`
`protected double`	`i20`
`protected double`	`i21`
`protected double`	`i22`
`protected double`	`i23`
`protected boolean`	`isInvertible`
`protected double`	`m00`
`protected double`	`m01`
`protected double`	`m02`
`protected double`	`m03`
`protected double`	`m10`
`protected double`	`m11`
`protected double`	`m12`
`protected double`	`m13`
`protected double`	`m20`
`protected double`	`m21`
`protected double`	`m22`
`protected double`	`m23`
`protected static int`	`MIN_NUM_MATCHES`
`protected double[][]`	`N`

Fields inherited from class mpicbg.models.AbstractModel
cost, rnd

Constructor Summary

Constructors
Constructor and Description

SimilarityModel3D()

Constructors
Constructor and Description
`SimilarityModel3D()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double[]`	`apply(double[] l)` Apply the `CoordinateTransform` to a location.
`void`	`applyInPlace(double[] l)` Apply the `CoordinateTransform` to a location.
`double[]`	`applyInverse(double[] l)` Apply the inverse of the model to a point location
`void`	`applyInverseInPlace(double[] l)` apply the inverse of the model to a point location
`boolean`	`canDoNumDimension(int numDimensions)`
`void`	`concatenate(SimilarityModel3D model)`
`SimilarityModel3D`	`copy()` Clone the model.
`SimilarityModel3D`	`createInverse()`
`<P extends PointMatch> void`	`fit(Collection<P> matches)` Fit the `Model` to a set of data points minimizing the global transfer error.
`void`	`fit(double[][] p, double[][] q, double[] w)` Default fit implementation using `Model.fit(Collection)`.
`void`	`fit(float[][] p, float[][] q, float[] w)` Default fit implementation using `Model.fit(Collection)`.
`double[]`	`getMatrix(double[] m)`
`int`	`getMinNumMatches()`
`protected void`	`invert()`
`void`	`preConcatenate(SimilarityModel3D model)`
`void`	`set(SimilarityModel3D m)` Set the model to m
`void`	`toArray(double[] data)` Write the 12 parameters of the affine into a double array.
`void`	`toMatrix(double[][] data)` Write the 12 parameters of the affine into a 4x3 double array.
`String`	`toString()`

Methods inherited from class mpicbg.models.AbstractAffineModel3D
estimateBounds, estimateInverseBounds

Methods inherited from class mpicbg.models.AbstractModel
betterThan, filter, filter, filter, filterRansac, filterRansac, filterRansac, filterRansac, getCost, icp, localSmoothnessFilter, ransac, ransac, setCost, test, test

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

Methods inherited from interface mpicbg.models.Boundable
estimateBounds

Methods inherited from interface mpicbg.models.InverseBoundable
estimateInverseBounds

- Field Detail
  - MIN_NUM_MATCHES
```
protected static final int MIN_NUM_MATCHES
```
    See Also:
    
    Constant Field Values
  - m00
```
protected double m00
```
  - m01
```
protected double m01
```
  - m02
```
protected double m02
```
  - m03
```
protected double m03
```
  - m10
```
protected double m10
```
  - m11
```
protected double m11
```
  - m12
```
protected double m12
```
  - m13
```
protected double m13
```
  - m20
```
protected double m20
```
  - m21
```
protected double m21
```
  - m22
```
protected double m22
```
  - m23
```
protected double m23
```
  - i00
```
protected double i00
```
  - i01
```
protected double i01
```
  - i02
```
protected double i02
```
  - i03
```
protected double i03
```
  - i10
```
protected double i10
```
  - i11
```
protected double i11
```
  - i12
```
protected double i12
```
  - i13
```
protected double i13
```
  - i20
```
protected double i20
```
  - i21
```
protected double i21
```
  - i22
```
protected double i22
```
  - i23
```
protected double i23
```
  - N
```
protected final double[][] N
```
  - isInvertible
```
protected boolean isInvertible
```
- Constructor Detail
  - SimilarityModel3D
```
public SimilarityModel3D()
```
- Method Detail
  - canDoNumDimension
```
public boolean canDoNumDimension(int numDimensions)
```
  - fit
```
public final void fit(float[][] p,
                      float[][] q,
                      float[] w)
               throws NotEnoughDataPointsException,
                      IllDefinedDataPointsException
```
    Description copied from class: AbstractModel
    
    Default fit implementation using Model.fit(Collection). This foils the intention that AbstractModel.fit(float[][], float[][], float[]) would be potentially more efficient. You should better implement it directly.
    
    Specified by:
    
    fit in interface Model<SimilarityModel3D>
    
    Overrides:
    
    fit in class AbstractModel<SimilarityModel3D>
    
    Parameters:
    
    p - source points
    
    q - target points
    
    w - weights
    
    Throws:
    
    NotEnoughDataPointsException - if not enough data points were available
    
    IllDefinedDataPointsException - if the set of data points is inappropriate to solve the Model
  - fit
```
public final void fit(double[][] p,
                      double[][] q,
                      double[] w)
               throws NotEnoughDataPointsException,
                      IllDefinedDataPointsException
```
    Description copied from class: AbstractModel
    
    Default fit implementation using Model.fit(Collection). This foils the intention that AbstractModel.fit(double[][], double[][], double[]) would be potentially more efficient. You should better implement it directly.
    
    Specified by:
    
    fit in interface Model<SimilarityModel3D>
    
    Overrides:
    
    fit in class AbstractModel<SimilarityModel3D>
    
    Parameters:
    
    p - source points
    
    q - target points
    
    w - weights
    
    Throws:
    
    NotEnoughDataPointsException - if not enough data points were available
    
    IllDefinedDataPointsException - if the set of data points is inappropriate to solve the Model
  - fit
```
public final <P extends PointMatch> void fit(Collection<P> matches)
                                      throws NotEnoughDataPointsException,
                                             IllDefinedDataPointsException
```
    Description copied from interface: Model
    
    Fit the Model to a set of data points minimizing the global transfer error. This is assumed to be implemented as a weighted least squares minimization. Use ransac and/ or Model.filter(java.util.Collection<P>, java.util.Collection<P>, double, int) to remove outliers from your data points.
    The estimated model transfers match.p1.local to match.p2.world.
    
    Specified by:
    
    fit in interface Model<SimilarityModel3D>
    
    Parameters:
    
    matches - set of point correpondences
    
    Throws:
    
    NotEnoughDataPointsException - if matches does not contain enough data points
    
    IllDefinedDataPointsException - if the set of data points is inappropriate to solve the Model
  - set
```
public final void set(SimilarityModel3D m)
```
    Description copied from interface: Model
    
    Set the model to m
    
    Specified by:
    
    set in interface Model<SimilarityModel3D>
  - copy
```
public SimilarityModel3D copy()
```
    Description copied from interface: Model
    
    Clone the model.
    
    Specified by:
    
    copy in interface Model<SimilarityModel3D>
  - getMinNumMatches
```
public final int getMinNumMatches()
```
    Specified by:
    
    getMinNumMatches in interface Model<SimilarityModel3D>
    
    Returns:
    
    the minimal number of PointMatches required to solve the model.
  - apply
```
public final double[] apply(double[] l)
```
    Description copied from interface: CoordinateTransform
    
    Apply the CoordinateTransform to a location.
    
    Specified by:
    
    apply in interface CoordinateTransform
    
    Returns:
    
    transformed location
  - applyInPlace
```
public final void applyInPlace(double[] l)
```
    Description copied from interface: CoordinateTransform
    
    Apply the CoordinateTransform to a location.
    
    Specified by:
    
    applyInPlace in interface CoordinateTransform
  - toString
```
public final String toString()
```
    Overrides:
    
    toString in class Object
  - invert
```
protected void invert()
```
  - applyInverse
```
public double[] applyInverse(double[] l)
                      throws NoninvertibleModelException
```
    Description copied from interface: InverseCoordinateTransform
    
    Apply the inverse of the model to a point location
    
    Specified by:
    
    applyInverse in interface InverseCoordinateTransform
    
    Returns:
    
    transformed point
    
    Throws:
    
    NoninvertibleModelException
  - applyInverseInPlace
```
public void applyInverseInPlace(double[] l)
                         throws NoninvertibleModelException
```
    Description copied from interface: InverseCoordinateTransform
    
    apply the inverse of the model to a point location
    
    Specified by:
    
    applyInverseInPlace in interface InverseCoordinateTransform
    
    Throws:
    
    NoninvertibleModelException
  - preConcatenate
```
public void preConcatenate(SimilarityModel3D model)
```
    Specified by:
    
    preConcatenate in interface Affine3D<SimilarityModel3D>
  - concatenate
```
public void concatenate(SimilarityModel3D model)
```
    Specified by:
    
    concatenate in interface Affine3D<SimilarityModel3D>
  - toArray
```
public void toArray(double[] data)
```
    Description copied from interface: Affine3D
    
    Write the 12 parameters of the affine into a double array. The order is m00, m10, m20, m01, m11, m21, m02, m12, m22, m03, m13, m23
    
    Specified by:
    
    toArray in interface Affine3D<SimilarityModel3D>
  - toMatrix
```
public void toMatrix(double[][] data)
```
    Description copied from interface: Affine3D
    Write the 12 parameters of the affine into a 4x3 double array. The order is
```
 [0][0] -> m00; [0][1] -> m01; [0][2] -> m02; [0][3] -> m03
 [1][0] -> m10; [1][1] -> m11; [1][2] -> m12; [1][3] -> m13
 [2][0] -> m20; [2][1] -> m21; [2][2] -> m22; [2][3] -> m23
 
```
    Specified by:
    
    toMatrix in interface Affine3D<SimilarityModel3D>
  - createInverse
```
public SimilarityModel3D createInverse()
```
    Specified by:
    
    createInverse in interface Affine3D<SimilarityModel3D>
    
    Specified by:
    
    createInverse in interface InvertibleCoordinateTransform
  - getMatrix
```
public double[] getMatrix(double[] m)
```
    Specified by:
    
    getMatrix in class AbstractAffineModel3D<SimilarityModel3D>

Class SimilarityModel3D

Field Summary

Fields inherited from class mpicbg.models.AbstractModel

Constructor Summary

Method Summary

Methods inherited from class mpicbg.models.AbstractAffineModel3D

Methods inherited from class mpicbg.models.AbstractModel

Methods inherited from class java.lang.Object

Methods inherited from interface mpicbg.models.Boundable

Methods inherited from interface mpicbg.models.InverseBoundable

Field Detail

MIN_NUM_MATCHES

m00

m01

m02

m03

m10

m11

m12

m13

m20

m21

m22

m23

i00

i01

i02

i03

i10

i11

i12

i13

i20

i21

i22

i23

N

isInvertible

Constructor Detail

SimilarityModel3D

Method Detail

canDoNumDimension

fit

fit

fit

set

copy

getMinNumMatches

apply

applyInPlace

toString

invert

applyInverse

applyInverseInPlace

preConcatenate

concatenate

toArray

toMatrix

createInverse

getMatrix