AffineModel3D (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.models.AbstractModel<M>
- - mpicbg.models.AbstractAffineModel3D<AffineModel3D>
  - - mpicbg.models.AffineModel3D

All Implemented Interfaces:

Serializable, Affine3D<AffineModel3D>, Boundable, CoordinateTransform, InverseBoundable, InverseCoordinateTransform, InvertibleBoundable, InvertibleCoordinateTransform, Model<AffineModel3D>

Direct Known Subclasses:

AffineModel3D
```
public class AffineModel3D
extends AbstractAffineModel3D<AffineModel3D>
implements InvertibleBoundable
```
3d-affine transformation models to be applied to points in 3d-space. This model includes the closed form weighted least squares solution as described by \citet{SchaeferAl06} transferred to 3d BibTeX:
```
 @article{SchaeferAl06,
   author    = {Scott Schaefer and Travis McPhail and Joe Warren},
   title     = {Image deformation using moving least squares},
   journal   = {ACM Transactions on Graphics},
   volume    = {25},
   number    = {3},
   year      = {2006},
   pages     = {533--540},
   publisher = {ACM},
   address   = {New York, NY, USA},
   url       = {http://faculty.cs.tamu.edu/schaefer/research/mls.pdf},
 }
 
```
Author:

Stephan Saalfeld <saalfelds@janelia.hhmi.org> and Johannes Schindelin

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`

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

Constructor Summary

Constructors
Constructor and Description

AffineModel3D()

Constructors
Constructor and Description
`AffineModel3D()`

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
`void`	`concatenate(AffineModel3D model)`
`void`	`concatenate(TranslationModel3D model)`
`AffineModel3D`	`copy()` Clone the model.
`AffineModel3D`	`createInverse()` TODO Not yet tested
`<P extends PointMatch> void`	`fit(Collection<P> matches)` Closed form weighted least squares solution as described by \citet{SchaeferAl06}.
`void`	`fit(double[][] p, double[][] q, double[] w)` Closed form weighted least squares solution as described by \citet{SchaeferAl06}.
`void`	`fit(float[][] p, float[][] q, float[] w)` Closed form weighted least squares solution as described by \citet{SchaeferAl06}.
`double[]`	`getMatrix(double[] m)`
`int`	`getMinNumMatches()`
`protected void`	`invert()`
`void`	`preConcatenate(AffineModel3D model)`
`void`	`preConcatenate(TranslationModel3D model)`
`void`	`reset()`
`void`	`rotate(int axis, double d)` Rotate
`void`	`set(AffineModel3D m)` Set the model to m
`void`	`set(double m00, double m01, double m02, double m03, double m10, double m11, double m12, double m13, double m20, double m21, double m22, double m23)` Initialize the model such that the respective affine transform is:
`void`	`set(RigidModel3D m)`
`void`	`set(SimilarityModel3D m)`
`void`	`set(TranslationModel3D 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
```
  - isInvertible
```
protected boolean isInvertible
```
- Constructor Detail
  - AffineModel3D
```
public AffineModel3D()
```
- Method Detail
  - getMatrix
```
public double[] getMatrix(double[] m)
```
    Specified by:
    
    getMatrix in class AbstractAffineModel3D<AffineModel3D>
  - getMinNumMatches
```
public final int getMinNumMatches()
```
    Specified by:
    
    getMinNumMatches in interface Model<AffineModel3D>
    
    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
  - applyInverse
```
public final 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 final 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
  - fit
```
public final void fit(double[][] p,
                      double[][] q,
                      double[] w)
               throws NotEnoughDataPointsException,
                      IllDefinedDataPointsException
```
    Closed form weighted least squares solution as described by \citet{SchaeferAl06}.
    
    Specified by:
    
    fit in interface Model<AffineModel3D>
    
    Overrides:
    
    fit in class AbstractModel<AffineModel3D>
    
    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(float[][] p,
                      float[][] q,
                      float[] w)
               throws NotEnoughDataPointsException,
                      IllDefinedDataPointsException
```
    Closed form weighted least squares solution as described by \citet{SchaeferAl06}.
    
    Specified by:
    
    fit in interface Model<AffineModel3D>
    
    Overrides:
    
    fit in class AbstractModel<AffineModel3D>
    
    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
```
    Closed form weighted least squares solution as described by \citet{SchaeferAl06}.
    
    Specified by:
    
    fit in interface Model<AffineModel3D>
    
    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(AffineModel3D m)
```
    Description copied from interface: Model
    
    Set the model to m
    
    Specified by:
    
    set in interface Model<AffineModel3D>
  - reset
```
public final void reset()
```
  - set
```
public final void set(TranslationModel3D m)
```
  - set
```
public final void set(RigidModel3D m)
```
  - set
```
public final void set(SimilarityModel3D m)
```
  - copy
```
public AffineModel3D copy()
```
    Description copied from interface: Model
    
    Clone the model.
    
    Specified by:
    
    copy in interface Model<AffineModel3D>
  - invert
```
protected void invert()
```
  - preConcatenate
```
public final void preConcatenate(AffineModel3D model)
```
    Specified by:
    
    preConcatenate in interface Affine3D<AffineModel3D>
  - concatenate
```
public final void concatenate(AffineModel3D model)
```
    Specified by:
    
    concatenate in interface Affine3D<AffineModel3D>
  - concatenate
```
public final void concatenate(TranslationModel3D model)
```
  - preConcatenate
```
public final void preConcatenate(TranslationModel3D model)
```
  - set
```
public final void set(double m00,
                      double m01,
                      double m02,
                      double m03,
                      double m10,
                      double m11,
                      double m12,
                      double m13,
                      double m20,
                      double m21,
                      double m22,
                      double m23)
```
    Initialize the model such that the respective affine transform is:
```
 m00 m01 m02 m03
 m10 m11 m12 m13
 m20 m21 m22 m23
 0   0   0   1
 
```
    Parameters:
    
    m00 -
    
    m01 -
    
    m02 -
    
    m03 -
    
    m10 -
    
    m11 -
    
    m12 -
    
    m13 -
    
    m20 -
    
    m21 -
    
    m22 -
    
    m23 -
  - toString
```
public final String toString()
```
    Overrides:
    
    toString in class Object
  - createInverse
```
public AffineModel3D createInverse()
```
    TODO Not yet tested
    
    Specified by:
    
    createInverse in interface Affine3D<AffineModel3D>
    
    Specified by:
    
    createInverse in interface InvertibleCoordinateTransform
  - rotate
```
public void rotate(int axis,
                   double d)
```
    Rotate
    
    Parameters:
    
    axis - 0=x, 1=y, 2=z
    
    d - angle in radians TODO Don't be lazy and do it directly on the values instead of creating another transform
  - 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<AffineModel3D>
  - 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<AffineModel3D>

Class AffineModel3D

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

isInvertible

Constructor Detail

AffineModel3D

Method Detail

getMatrix

getMinNumMatches

apply

applyInPlace

applyInverse

applyInverseInPlace

fit

fit

fit

set

reset

set

set

set

copy

invert

preConcatenate

concatenate

concatenate

preConcatenate

set

toString

createInverse

rotate

toArray

toMatrix