TransformMesh (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.models.TransformMesh

All Implemented Interfaces:

Serializable, CoordinateTransform, InverseCoordinateTransform, InvertibleCoordinateTransform

Direct Known Subclasses:

CoordinateTransformMesh, MovingLeastSquaresMesh, SpringMesh, TransformMesh
```
public class TransformMesh
extends Object
implements InvertibleCoordinateTransform
```
Triangular transformation mesh.
See an example to find out how the mesh is constructed:

numX = 4; numY = 3:
```
 *---*---*---*
 |\ / \ / \ /|
 | *---*---* |
 |/ \ / \ / \|
 *---*---*---*
 |\ / \ / \ /|
 | *---*---* |
 |/ \ / \ / \|
 *---*---*---*
 
```
Each vertex is given as a PointMatch with p1 being the original point and p2 being the transferred point. Keep in mind that Points store local and world coordinates with local coordinates being constant and world coordinates being mutable. That is initially p1.l = p1.w = p2.l while p1.w is the transferred location of the vertex.

Three adjacent vertices span a triangle. All pixels inside a triangle will be transferred by a 2d affine transform that is defined by the three vertices. Given the abovementioned definition of a vertex as PointMatch, this 2d affine transform is a forward transform (p1.l->p2.w).
Author:

Stephan Saalfeld <saalfelds@janelia.hhmi.org>

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`protected HashMap<AffineModel2D,ArrayList<PointMatch>>`	`av`
`protected static PointFactory<Point>`	`defaultPointFactory`
`protected static PointMatchFactory<PointMatch>`	`defaultPointMatchFactory`
`protected double`	`height`
`protected HashMap<PointMatch,ArrayList<AffineModel2D>>`	`va`
`protected double`	`width`

Constructor Summary

Constructors
Modifier	Constructor and Description
	`TransformMesh(int numX, double width, double height)`
	`TransformMesh(int numX, int numY, double width, double height)`
`protected`	`TransformMesh(int numX, int numY, double width, double height, PointFactory<?> pointFactory, PointMatchFactory<?> pointMatchFactory)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addTriangle(ArrayList<PointMatch> t)` Add a triangle defined by 3 PointMatches that defines an AffineTransform2D.
`double[]`	`apply(double[] location)` Apply the `CoordinateTransform` to a location.
`void`	`applyInPlace(double[] location)` Apply the `CoordinateTransform` to a location.
`double[]`	`applyInverse(double[] location)` Apply the inverse of the model to a point location
`void`	`applyInverseInPlace(double[] location)` apply the inverse of the model to a point location
`void`	`bounds(double[] min, double[] max)` Calculate bounding box
`TransformMesh`	`createInverse()` TODO Not yet tested
`PointMatch`	`findClosestSourcePoint(double[] there)` Find the closest source point to a given coordinate.
`PointMatch`	`findClosestTargetPoint(double[] there)` Find the closest target point to a given coordinate.
`HashMap<AffineModel2D,ArrayList<PointMatch>>`	`getAV()`
`double`	`getHeight()`
`HashMap<PointMatch,ArrayList<AffineModel2D>>`	`getVA()`
`double`	`getWidth()`
`String`	`illustrateBestRigidSVG()` Create an SVG path that illustrates the best regid approximation of the mesh as a rotated square.
`Shape`	`illustrateMesh()` Create a Shape that illustrates the mesh.
`String`	`illustrateMeshSVG()` Create an SVG path that illustrates the mesh.
`protected void`	`illustrateTriangle(AffineModel2D ai, GeneralPath path)`
`void`	`init(CoordinateTransform t)` Initialize the mesh with a `CoordinateTransform`.
`static boolean`	`isInConvexTargetPolygon(ArrayList<PointMatch> pm, double[] t)` Checks if a location is inside a given polygon at the target side or not.
`static boolean`	`isInSourcePolygon(ArrayList<PointMatch> pm, double[] t)` Checks if a location is inside a given polygon at the source side or not.
`protected static int`	`numY(int numX, double width, double height)`
`void`	`scale(double scale)` Scale all vertex coordinates
`void`	`updateAffine(PointMatch p)` Update all affine transformations that would have been affected by a given `Vertex`.
`void`	`updateAffines()` Update all affine transformations.

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

- Field Detail
  - width
```
protected final double width
```
  - height
```
protected final double height
```
  - av
```
protected final HashMap<AffineModel2D,ArrayList<PointMatch>> av
```
  - va
```
protected final HashMap<PointMatch,ArrayList<AffineModel2D>> va
```
  - defaultPointFactory
```
protected static final PointFactory<Point> defaultPointFactory
```
  - defaultPointMatchFactory
```
protected static final PointMatchFactory<PointMatch> defaultPointMatchFactory
```
- Constructor Detail
  - TransformMesh
```
protected TransformMesh(int numX,
                        int numY,
                        double width,
                        double height,
                        PointFactory<?> pointFactory,
                        PointMatchFactory<?> pointMatchFactory)
```
  - TransformMesh
```
public TransformMesh(int numX,
                     int numY,
                     double width,
                     double height)
```
  - TransformMesh
```
public TransformMesh(int numX,
                     double width,
                     double height)
```
- Method Detail
  - getWidth
```
public double getWidth()
```
  - getHeight
```
public double getHeight()
```
  - getAV
```
public HashMap<AffineModel2D,ArrayList<PointMatch>> getAV()
```
  - getVA
```
public HashMap<PointMatch,ArrayList<AffineModel2D>> getVA()
```
  - numY
```
protected static final int numY(int numX,
                                double width,
                                double height)
```
  - addTriangle
```
public void addTriangle(ArrayList<PointMatch> t)
```
    Add a triangle defined by 3 PointMatches that defines an AffineTransform2D.
    
    Parameters:
    
    t - 3 PointMatches (will not be copied, so do not reuse this list!)
  - illustrateTriangle
```
protected void illustrateTriangle(AffineModel2D ai,
                                  GeneralPath path)
```
  - illustrateMesh
```
public Shape illustrateMesh()
```
    Create a Shape that illustrates the mesh.
    
    Returns:
    
    the illustration
  - illustrateMeshSVG
```
public String illustrateMeshSVG()
```
    Create an SVG path that illustrates the mesh.
    
    Returns:
    
    svg path-definition
  - illustrateBestRigidSVG
```
public String illustrateBestRigidSVG()
```
    Create an SVG path that illustrates the best regid approximation of the mesh as a rotated square.
    
    Returns:
    
    svg path-definition
  - updateAffine
```
public void updateAffine(PointMatch p)
```
    Update all affine transformations that would have been affected by a given Vertex.
    
    Parameters:
    
    p -
  - updateAffines
```
public void updateAffines()
```
    Update all affine transformations.
  - findClosestSourcePoint
```
public PointMatch findClosestSourcePoint(double[] there)
```
    Find the closest source point to a given coordinate. Each vertex being defined by a PointMatch, the source coordinates are the local coordinates of the source point.
    
    Parameters:
    
    there -
    
    Returns:
    
    closest PointMatch in terms of the source point
  - findClosestTargetPoint
```
public PointMatch findClosestTargetPoint(double[] there)
```
    Find the closest target point to a given coordinate. Each vertex being defined by a PointMatch, the target coordinates are the world coordinates of the target point.
    
    Parameters:
    
    there -
    
    Returns:
    
    closest PointMatch in terms of the target point
  - isInConvexTargetPolygon
```
public static boolean isInConvexTargetPolygon(ArrayList<PointMatch> pm,
                                              double[] t)
```
    Checks if a location is inside a given polygon at the target side or not.
    
    Parameters:
    
    pm -
    
    t -
    
    Returns:
  - isInSourcePolygon
```
public static final boolean isInSourcePolygon(ArrayList<PointMatch> pm,
                                              double[] t)
```
    Checks if a location is inside a given polygon at the source side or not.
    
    Parameters:
    
    pm -
    
    t -
    
    Returns:
  - apply
```
public double[] apply(double[] location)
```
    Description copied from interface: CoordinateTransform
    
    Apply the CoordinateTransform to a location.
    
    Specified by:
    
    apply in interface CoordinateTransform
    
    Returns:
    
    transformed location
  - applyInPlace
```
public void applyInPlace(double[] location)
```
    Description copied from interface: CoordinateTransform
    
    Apply the CoordinateTransform to a location.
    
    Specified by:
    
    applyInPlace in interface CoordinateTransform
  - applyInverse
```
public double[] applyInverse(double[] location)
                      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[] location)
                         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
  - createInverse
```
public TransformMesh createInverse()
```
    TODO Not yet tested
    
    Specified by:
    
    createInverse in interface InvertibleCoordinateTransform
  - init
```
public void init(CoordinateTransform t)
```
    Initialize the mesh with a CoordinateTransform.
    
    Parameters:
    
    t -
  - scale
```
public void scale(double scale)
```
    Scale all vertex coordinates
    
    Parameters:
    
    scale -
  - bounds
```
public void bounds(double[] min,
                   double[] max)
```
    Calculate bounding box
    
    Parameters:
    
    min -
    
    max -

Class TransformMesh

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

width

height

av

va

defaultPointFactory

defaultPointMatchFactory

Constructor Detail

TransformMesh

TransformMesh

TransformMesh

Method Detail

getWidth

getHeight

getAV

getVA

numY

addTriangle

illustrateTriangle

illustrateMesh

illustrateMeshSVG

illustrateBestRigidSVG

updateAffine

updateAffines

findClosestSourcePoint

findClosestTargetPoint

isInConvexTargetPolygon

isInSourcePolygon

apply

applyInPlace

applyInverse

applyInverseInPlace

createInverse

init

scale

bounds