SpringMesh (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.models.TransformMesh
- - mpicbg.models.SpringMesh

All Implemented Interfaces:

Serializable, CoordinateTransform, InverseCoordinateTransform, InvertibleCoordinateTransform
```
public class SpringMesh
extends TransformMesh
```
A TransformMesh with all Vertices being interconnected by springs. It implements the optimization straightforward as a dynamic process. A SpringMesh may or may not contain passive vertices that are not connected to other vertices of the mesh itself. Depending on their location, such passive vertices are moved by the respective AffineModel2D. Passive vertices are used to uni-directionally connect two SpringMeshes.

Author:

Stephan Saalfeld <saalfelds@janelia.hhmi.org>

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`protected HashMap<AffineModel2D,Vertex>`	`apv`
`protected double`	`damp`
`protected HashSet<Vertex>`	`fixedVertices`
`protected double`	`force`
`protected double`	`maxForce`
`protected double`	`maxSpeed`
`protected double`	`minForce`
`protected HashMap<PointMatch,Vertex>`	`pv`
`protected HashMap<Vertex,AffineModel2D>`	`pva`
`protected ArrayList<Vertex>`	`vertices`
`protected HashMap<Vertex,PointMatch>`	`vp`

Fields inherited from class mpicbg.models.TransformMesh
av, defaultPointFactory, defaultPointMatchFactory, height, va, width

Constructor Summary

Constructors
Constructor and Description
`SpringMesh(int numX, double width, double height, double springWeight, double maxStretch, double damp)`
`SpringMesh(int numX, int numY, double width, double height, double springWeight, double maxStretch, double damp)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`addPassiveVertex(Vertex vertex)` Add a passive vertex.
`void`	`addVertex(Vertex vertex, double weight)` Add a `Vertex` to the mesh.
`void`	`addVertexWeightedByDistance(Vertex vertex, double weight, double alpha)` Add a `Vertex` to the mesh.
`protected void`	`calculateForceAndSpeed(ErrorStatistic observer)` Deprecated. Remains for legacy compatibility
`Vertex`	`findClosestSourceVertex(double[] there)` Find the closest `Vertex` to a given coordinate in terms of its source coordinates.
`Vertex`	`findClosestTargetVertex(double[] there)` Find the closest `Vertex` to a given coordinate in terms of its target coordinates.
`double`	`getForce()`
`ArrayList<Vertex>`	`getVertices()`
`Shape`	`illustrateMesh()` Create a Shape that illustrates the mesh.
`Shape`	`illustrateSprings()` Create a Shape that illustrates the `Spring`s.
`void`	`illustrateSprings(ij.process.ColorProcessor ip, double scale, double maxStretch)` Paint all `Spring`s into a `ColorProcessor`.
`void`	`illustrateSprings(ij.process.ColorProcessor ip, double scale, double maxStretch, double offsetX, double offsetY)` Paint all `Springs` into a `ColorProcessor`.
`void`	`init(CoordinateTransform t)` TODO Not yet tested
`int`	`numVertices()`
`void`	`optimize(double maxError, int maxIterations, int maxPlateauwidth)` Optimize the mesh.
`static void`	`optimizeMeshes(Collection<SpringMesh> meshes, double maxError, int maxIterations, int maxPlateauwidth)` Optimize a `Collection` of connected `SpringMeshes`.
`static void`	`optimizeMeshes(Collection<SpringMesh> meshes, double maxError, int maxIterations, int maxPlateauwidth, boolean visualize)` Optimize a `Collection` of connected `SpringMeshes`.
`static void`	`optimizeMeshes(Collection<SpringMesh> meshes, double maxError, int maxIterations, int maxPlateauwidth, double maxStepSize, boolean visualize)` Optimize a `Collection` of connected `SpringMeshes`.
`static void`	`optimizeMeshes2(Collection<SpringMesh> meshes, double maxError, int maxIterations, int maxPlateauwidth)` Deprecated. Remains for reproducing legacy results
`static void`	`optimizeMeshes2(Collection<SpringMesh> meshes, double maxError, int maxIterations, int maxPlateauwidth, boolean visualize)` Deprecated. Remains for reproducing legacy results
`protected void`	`optimizeStep(ErrorStatistic observer)` Performs one optimization step.
`static ij.process.ColorProcessor`	`paintMeshes(Collection<SpringMesh> meshes, double scale)`
`static ij.process.ColorProcessor`	`paintSprings(Collection<SpringMesh> meshes, double scale, double maxStretch)`
`static ij.process.ColorProcessor`	`paintSprings(Collection<SpringMesh> meshes, int width, int height, double maxStretch)`
`protected static void`	`println(String s)`
`void`	`removePassiveVertex(Vertex vertex)` Remove a passive vertex.
`void`	`scale(double scale)` TODO Not yet tested
`protected void`	`update(double dt)` Move all vertices for a given Δt
`void`	`updateAffines()` Update all affine transformations.
`protected void`	`updateDirection(double dt)` Calculate motion vectors for all vertices.
`protected void`	`updateForce(ErrorStatistic observer)` Update force vectors for all vertices.
`void`	`updatePassiveVertices()`
`protected double`	`weigh(double d, double alpha)`

Methods inherited from class mpicbg.models.TransformMesh
addTriangle, apply, applyInPlace, applyInverse, applyInverseInPlace, bounds, createInverse, findClosestSourcePoint, findClosestTargetPoint, getAV, getHeight, getVA, getWidth, illustrateBestRigidSVG, illustrateMeshSVG, illustrateTriangle, isInConvexTargetPolygon, isInSourcePolygon, numY, updateAffine

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

Field Detail

fixedVertices

protected final HashSet<Vertex> fixedVertices

vertices

protected final ArrayList<Vertex> vertices

vp

protected final HashMap<Vertex,PointMatch> vp

pv

protected final HashMap<PointMatch,Vertex> pv

apv

protected final HashMap<AffineModel2D,Vertex> apv

pva

protected final HashMap<Vertex,AffineModel2D> pva

force
```
protected double force
```

minForce
```
protected double minForce
```

maxForce
```
protected double maxForce
```

maxSpeed
```
protected double maxSpeed
```

damp
```
protected double damp
```

Constructor Detail

SpringMesh

public SpringMesh(int numX,
                  int numY,
                  double width,
                  double height,
                  double springWeight,
                  double maxStretch,
                  double damp)

SpringMesh

public SpringMesh(int numX,
                  double width,
                  double height,
                  double springWeight,
                  double maxStretch,
                  double damp)

Method Detail
- getVertices
```
public ArrayList<Vertex> getVertices()
```
- numVertices
```
public int numVertices()
```
- getForce
```
public double getForce()
```
- weigh
```
protected double weigh(double d,
                       double alpha)
```
- println
```
protected static void println(String s)
```
- findClosestTargetVertex
```
public final Vertex findClosestTargetVertex(double[] there)
```
  Find the closest Vertex to a given coordinate in terms of its target coordinates.
  
  Parameters:
  
  there -
  
  Returns:
  
  closest Vertex
- findClosestSourceVertex
```
public final Vertex findClosestSourceVertex(double[] there)
```
  Find the closest Vertex to a given coordinate in terms of its source coordinates.
  
  Parameters:
  
  there -
  
  Returns:
  
  closest Vertex
- addPassiveVertex
```
public void addPassiveVertex(Vertex vertex)
```
  Add a passive vertex. Associate it with the triangle by whom it is contained.
  
  Parameters:
  
  vertex -
- removePassiveVertex
```
public void removePassiveVertex(Vertex vertex)
```
  Remove a passive vertex.
  
  Parameters:
  
  vertex -
- addVertex
```
public void addVertex(Vertex vertex,
                      double weight)
```
  Add a Vertex to the mesh. Connect it to the closest vertex of the actual mesh by a spring with the given weight.
  
  Parameters:
  
  vertex -
  
  weight -
- addVertexWeightedByDistance
```
public final void addVertexWeightedByDistance(Vertex vertex,
                                              double weight,
                                              double alpha)
```
  Add a Vertex to the mesh. Connect it to all other Vertices by springs that are weighted by their length. The weight is defined by 1/(l^2*alpha)
  
  Parameters:
  
  vertex -
  
  weight -
  
  alpha -
- updateForce
```
protected void updateForce(ErrorStatistic observer)
```
  Update force vectors for all vertices.
  
  Parameters:
  
  observer -
- updateDirection
```
protected void updateDirection(double dt)
```
  Calculate motion vectors for all vertices.
  
  Parameters:
  
  dt -
- update
```
protected void update(double dt)
```
  Move all vertices for a given Δt
  
  Parameters:
  
  dt -
- optimizeStep
```
protected void optimizeStep(ErrorStatistic observer)
                     throws NotEnoughDataPointsException
```
  Performs one optimization step.
  
  Parameters:
  
  observer - collecting the error after update
  
  Throws:
  
  NotEnoughDataPointsException
- updatePassiveVertices
```
public void updatePassiveVertices()
```
- updateAffines
```
public void updateAffines()
```
  Description copied from class: TransformMesh
  
  Update all affine transformations.
  
  Overrides:
  
  updateAffines in class TransformMesh
- optimize
```
public void optimize(double maxError,
                     int maxIterations,
                     int maxPlateauwidth)
              throws NotEnoughDataPointsException
```
  Optimize the mesh.
  
  Parameters:
  
  maxError - do not accept convergence if error is > max_error
  
  maxIterations - stop after that many iterations even if there was no minimum found
  
  maxPlateauwidth - convergence is reached if the average slope in an interval of this size is 0.0 (in double accuracy). This prevents the algorithm from stopping at plateaus smaller than this value.
  
  Throws:
  
  NotEnoughDataPointsException
- paintMeshes
```
public static final ij.process.ColorProcessor paintMeshes(Collection<SpringMesh> meshes,
                                                          double scale)
```
- paintSprings
```
public static final ij.process.ColorProcessor paintSprings(Collection<SpringMesh> meshes,
                                                           double scale,
                                                           double maxStretch)
```
- paintSprings
```
public static final ij.process.ColorProcessor paintSprings(Collection<SpringMesh> meshes,
                                                           int width,
                                                           int height,
                                                           double maxStretch)
```
- optimizeMeshes
```
public static void optimizeMeshes(Collection<SpringMesh> meshes,
                                  double maxError,
                                  int maxIterations,
                                  int maxPlateauwidth)
                           throws NotEnoughDataPointsException
```
  Optimize a Collection of connected SpringMeshes.
  
  Parameters:
  
  maxError - do not accept convergence if error is > max_error
  
  maxIterations - stop after that many iterations even if there was no minimum found
  
  maxPlateauwidth - convergence is reached if the average slope in an interval of this size is 0.0 (in double accuracy). This prevents the algorithm from stopping at plateaus smaller than this value.
  
  Throws:
  
  NotEnoughDataPointsException
- optimizeMeshes
```
public static void optimizeMeshes(Collection<SpringMesh> meshes,
                                  double maxError,
                                  int maxIterations,
                                  int maxPlateauwidth,
                                  boolean visualize)
                           throws NotEnoughDataPointsException
```
  Optimize a Collection of connected SpringMeshes.
  
  Parameters:
  
  maxError - do not accept convergence if error is > max_error
  
  maxIterations - stop after that many iterations even if there was no minimum found
  
  maxPlateauwidth - convergence is reached if the average slope in an interval of this size is 0.0 (in double accuracy). This prevents the algorithm from stopping at plateaus smaller than this value.
  
  Throws:
  
  NotEnoughDataPointsException
- optimizeMeshes
```
public static void optimizeMeshes(Collection<SpringMesh> meshes,
                                  double maxError,
                                  int maxIterations,
                                  int maxPlateauwidth,
                                  double maxStepSize,
                                  boolean visualize)
                           throws NotEnoughDataPointsException
```
  Optimize a Collection of connected SpringMeshes.
  
  Parameters:
  
  maxError - do not accept convergence if error is > max_error
  
  maxIterations - stop after that many iterations even if there was no minimum found
  
  maxPlateauwidth - convergence is reached if the average slope in an interval of this size is 0.0 (in double accuracy). This prevents the algorithm from stopping at plateaus smaller than this value.
  
  Throws:
  
  NotEnoughDataPointsException
- calculateForceAndSpeed
```
@Deprecated
protected void calculateForceAndSpeed(ErrorStatistic observer)
```
  Deprecated. Remains for legacy compatibility
  
  Calculate force and speed vectors for all vertices.
  
  Parameters:
  
  observer -
- optimizeMeshes2
```
@Deprecated
public static void optimizeMeshes2(Collection<SpringMesh> meshes,
                                               double maxError,
                                               int maxIterations,
                                               int maxPlateauwidth)
                                        throws NotEnoughDataPointsException
```
  Deprecated. Remains for reproducing legacy results
  
  Optimize a Collection of connected SpringMeshes.
  
  Parameters:
  
  maxError - do not accept convergence if error is > max_error
  
  maxIterations - stop after that many iterations even if there was no minimum found
  
  maxPlateauwidth - convergence is reached if the average slope in an interval of this size is 0.0 (in double accuracy). This prevents the algorithm from stopping at plateaus smaller than this value.
  
  Throws:
  
  NotEnoughDataPointsException
- optimizeMeshes2
```
@Deprecated
public static void optimizeMeshes2(Collection<SpringMesh> meshes,
                                               double maxError,
                                               int maxIterations,
                                               int maxPlateauwidth,
                                               boolean visualize)
                                        throws NotEnoughDataPointsException
```
  Deprecated. Remains for reproducing legacy results
  
  Optimize a Collection of connected SpringMeshes.
  
  Parameters:
  
  maxError - do not accept convergence if error is > max_error
  
  maxIterations - stop after that many iterations even if there was no minimum found
  
  maxPlateauwidth - convergence is reached if the average slope in an interval of this size is 0.0 (in double accuracy). This prevents the algorithm from stopping at plateaus smaller than this value.
  
  Throws:
  
  NotEnoughDataPointsException
- illustrateSprings
```
public Shape illustrateSprings()
```
  Create a Shape that illustrates the Springs.
  
  Returns:
  
  illustration
- illustrateSprings
```
public void illustrateSprings(ij.process.ColorProcessor ip,
                              double scale,
                              double maxStretch)
```
  Paint all Springs into a ColorProcessor.
- illustrateSprings
```
public void illustrateSprings(ij.process.ColorProcessor ip,
                              double scale,
                              double maxStretch,
                              double offsetX,
                              double offsetY)
```
  Paint all Springs into a ColorProcessor.
- illustrateMesh
```
public Shape illustrateMesh()
```
  Create a Shape that illustrates the mesh.
  
  Overrides:
  
  illustrateMesh in class TransformMesh
  
  Returns:
  
  the illustration
- init
```
public void init(CoordinateTransform t)
```
  TODO Not yet tested
  
  Overrides:
  
  init in class TransformMesh
- scale
```
public void scale(double scale)
```
  TODO Not yet tested
  
  Overrides:
  
  scale in class TransformMesh

Class SpringMesh

Field Summary

Fields inherited from class mpicbg.models.TransformMesh

Constructor Summary

Method Summary

Methods inherited from class mpicbg.models.TransformMesh

Methods inherited from class java.lang.Object

Field Detail

fixedVertices

vertices

vp

pv

apv

pva

force

minForce

maxForce

maxSpeed

damp

Constructor Detail

SpringMesh

SpringMesh

Method Detail

getVertices

numVertices

getForce

weigh

println

findClosestTargetVertex

findClosestSourceVertex

addPassiveVertex

removePassiveVertex

addVertex

addVertexWeightedByDistance

updateForce

updateDirection

update

optimizeStep

updatePassiveVertices

updateAffines

optimize

paintMeshes

paintSprings

paintSprings

optimizeMeshes

optimizeMeshes

optimizeMeshes

calculateForceAndSpeed

optimizeMeshes2

optimizeMeshes2

illustrateSprings

illustrateSprings

illustrateSprings

illustrateMesh

init

scale