TileConfiguration (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.models.TileConfiguration

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

TileConfiguration, TileConfigurationPhaseCorrelation, TileConfigurationStitching
```
public class TileConfiguration
extends Object
implements Serializable
```
A configuration of tiles. Add all tiles that build a common interconnectivity graph to one configuration, fix at least one of the tiles and optimize the configuration.

Author:

Stephan Saalfeld <saalfelds@janelia.hhmi.org>

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`protected static DecimalFormat`	`decimalFormat`
`protected static DecimalFormatSymbols`	`decimalFormatSymbols`
`protected double`	`error`
`protected HashSet<Tile<?>>`	`fixedTiles`
`protected double`	`maxError`
`protected double`	`minError`
`protected HashSet<Tile<?>>`	`tiles`

Constructor Summary

Constructors
Constructor and Description

TileConfiguration()

Constructors
Constructor and Description
`TileConfiguration()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addTile(Tile<?> t)` Add a single `Tile`.
`void`	`addTiles(Collection<? extends Tile<?>> t)` Add a `Collection` of `Tiles`.
`void`	`addTiles(TileConfiguration t)` Add all `Tiles` of another `TileConfiguration`.
`protected void`	`apply()` Apply the model of each `Tile` to all its `PointMatches`.
`void`	`clear()` Cleanup.
`void`	`fixTile(Tile<?> t)` Fix a single `Tile`.
`ArrayList<PointMatch>`	`getConnectingPointMatches(Tile<?> targetTile, Tile<?> referenceTile)` Returns an `ArrayList` of `PointMatch` that connect the targetTile and the referenceTile.
`double`	`getError()`
`HashSet<Tile<?>>`	`getFixedTiles()`
`double`	`getMaxError()`
`double`	`getMinError()`
`HashSet<Tile<?>>`	`getTiles()`
`void`	`optimize(double maxAllowedError, int maxIterations, int maxPlateauwidth)` Minimize the displacement of all `Correspondence pairs` of all `Tiles` and tell about it.
`void`	`optimize(double maxAllowedError, int maxIterations, int maxPlateauwidth, double damp)` Minimize the displacement of all `Correspondence pairs` of all `Tiles` and tell about it.
`void`	`optimize(ErrorStatistic observer, double maxAllowedError, int maxIterations, int maxPlateauwidth, double damp)` Minimize the displacement of all `Correspondence pairs` of all `Tiles` and tell about it.
`void`	`optimizeAndFilter(double maxAllowedError, int maxIterations, int maxPlateauwidth, double maxMeanFactor)`
`void`	`optimizeAndFilter(double maxAllowedError, int maxIterations, int maxPlateauwidth, double damp, double maxMeanFactor)`
`void`	`optimizeSilently(ErrorStatistic observer, double maxAllowedError, int maxIterations, int maxPlateauwidth)` Minimize the displacement of all `Correspondence pairs` of all `Tiles`
`void`	`optimizeSilently(ErrorStatistic observer, double maxAllowedError, int maxIterations, int maxPlateauwidth, double damp)` Minimize the displacement of all `Correspondence pairs` of all `Tiles`
`void`	`optimizeSilentlyConcurrent(ErrorStatistic observer, double maxAllowedError, int maxIterations, int maxPlateauwidth, double damp)`
`List<Tile<?>>`	`preAlign()` Computes a pre-alignemnt of all non-fixed `Tile`s by propagating the pairwise models.
`protected void`	`println(String s)`
`protected void`	`update()` Update all `Correspondences` in all `Tiles` and estimate the average displacement.
`protected void`	`updateErrors()` Estimate min/max/average displacement of all `PointMatches` in all `Tiles`.

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

Field Detail

decimalFormat

protected static final DecimalFormat decimalFormat

decimalFormatSymbols

protected static final DecimalFormatSymbols decimalFormatSymbols

tiles
```
protected final HashSet<Tile<?>> tiles
```

fixedTiles

protected final HashSet<Tile<?>> fixedTiles

minError
```
protected double minError
```

maxError
```
protected double maxError
```

error
```
protected double error
```

Constructor Detail
- TileConfiguration
```
public TileConfiguration()
```

Method Detail

getTiles

public final HashSet<Tile<?>> getTiles()

getFixedTiles

public final HashSet<Tile<?>> getFixedTiles()

getMinError
```
public final double getMinError()
```

getMaxError
```
public final double getMaxError()
```

getError
```
public final double getError()
```

println
```
protected void println(String s)
```

clear
```
public void clear()
```
Cleanup.

addTile
```
public void addTile(Tile<?> t)
```
Add a single Tile.

Parameters:

t -

addTiles

public void addTiles(Collection<? extends Tile<?>> t)

Add a Collection of Tiles.

Parameters:: t -

addTiles
```
public void addTiles(TileConfiguration t)
```
Add all Tiles of another TileConfiguration.

Parameters:

t -

fixTile
```
public void fixTile(Tile<?> t)
```
Fix a single Tile.

Parameters:

t -

apply
```
protected void apply()
```
Apply the model of each Tile to all its PointMatches.

updateErrors
```
protected void updateErrors()
```
Estimate min/max/average displacement of all PointMatches in all Tiles.

update
```
protected void update()
```
Update all Correspondences in all Tiles and estimate the average displacement.

optimizeSilently
```
public void optimizeSilently(ErrorStatistic observer,
                             double maxAllowedError,
                             int maxIterations,
                             int maxPlateauwidth)
                      throws NotEnoughDataPointsException,
                             IllDefinedDataPointsException
```
Minimize the displacement of all Correspondence pairs of all Tiles

Parameters:

maxAllowedError - 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 absolute slope in an interval of this size and half this size is smaller than 0.0001 (in double accuracy). This is assumed to prevent the algorithm from stopping at plateaus smaller than this value.

Throws:

NotEnoughDataPointsException

IllDefinedDataPointsException

optimizeSilently
```
public void optimizeSilently(ErrorStatistic observer,
                             double maxAllowedError,
                             int maxIterations,
                             int maxPlateauwidth,
                             double damp)
                      throws NotEnoughDataPointsException,
                             IllDefinedDataPointsException
```
Minimize the displacement of all Correspondence pairs of all Tiles

Parameters:

maxAllowedError - 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 absolute slope in an interval of this size and half this size is smaller than 0.0001 (in double accuracy). This is assumed to prevent the algorithm from stopping at plateaus smaller than this value.

Throws:

NotEnoughDataPointsException

IllDefinedDataPointsException

optimizeSilentlyConcurrent

public void optimizeSilentlyConcurrent(ErrorStatistic observer,
                                       double maxAllowedError,
                                       int maxIterations,
                                       int maxPlateauwidth,
                                       double damp)
                                throws NotEnoughDataPointsException,
                                       IllDefinedDataPointsException,
                                       InterruptedException,
                                       ExecutionException

Throws:: NotEnoughDataPointsException; IllDefinedDataPointsException; InterruptedException; ExecutionException

optimize

public void optimize(double maxAllowedError,
                     int maxIterations,
                     int maxPlateauwidth,
                     double damp)
              throws NotEnoughDataPointsException,
                     IllDefinedDataPointsException

Minimize the displacement of all Correspondence pairs of all Tiles and tell about it.

Parameters:: maxAllowedError -; maxIterations -; maxPlateauwidth -
Throws:: NotEnoughDataPointsException; IllDefinedDataPointsException

optimize

public void optimize(double maxAllowedError,
                     int maxIterations,
                     int maxPlateauwidth)
              throws NotEnoughDataPointsException,
                     IllDefinedDataPointsException

Minimize the displacement of all Correspondence pairs of all Tiles and tell about it.

Parameters:: maxAllowedError -; maxIterations -; maxPlateauwidth -
Throws:: NotEnoughDataPointsException; IllDefinedDataPointsException

optimize

public void optimize(ErrorStatistic observer,
                     double maxAllowedError,
                     int maxIterations,
                     int maxPlateauwidth,
                     double damp)
              throws NotEnoughDataPointsException,
                     IllDefinedDataPointsException

Minimize the displacement of all Correspondence pairs of all Tiles and tell about it.

Parameters:: maxAllowedError -; maxIterations -; maxPlateauwidth -
Throws:: NotEnoughDataPointsException; IllDefinedDataPointsException

optimizeAndFilter

public void optimizeAndFilter(double maxAllowedError,
                              int maxIterations,
                              int maxPlateauwidth,
                              double damp,
                              double maxMeanFactor)
                       throws NotEnoughDataPointsException,
                              IllDefinedDataPointsException

Throws:: NotEnoughDataPointsException; IllDefinedDataPointsException

optimizeAndFilter

public void optimizeAndFilter(double maxAllowedError,
                              int maxIterations,
                              int maxPlateauwidth,
                              double maxMeanFactor)
                       throws NotEnoughDataPointsException,
                              IllDefinedDataPointsException

Throws:: NotEnoughDataPointsException; IllDefinedDataPointsException

preAlign
```
public List<Tile<?>> preAlign()
                       throws NotEnoughDataPointsException,
                              IllDefinedDataPointsException
```
Computes a pre-alignemnt of all non-fixed Tiles by propagating the pairwise models. This does not give a correct registration but a very good starting point for the global optimization. This is necessary for models where the global optimization is not guaranteed to converge like the HomographyModel2D, RigidModel3D, ...

Returns:

- a list of Tiles that could not be pre-aligned

Throws:

NotEnoughDataPointsException

IllDefinedDataPointsException

getConnectingPointMatches
```
public ArrayList<PointMatch> getConnectingPointMatches(Tile<?> targetTile,
                                                       Tile<?> referenceTile)
```
Returns an ArrayList of PointMatch that connect the targetTile and the referenceTile. The order of the PointMatch is PointMatch.p1 = target, PointMatch.p2 = reference. A Model.fit() will then solve the fit so that target.p1.l is mapped to reference.p2.w.

Parameters:

targetTile - - the Tile for which a Model can fit

referenceTile - - the Tile to which target will map

Returns:

- an ArrayList of all PointMatch that target and reference share

Class TileConfiguration

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

decimalFormat

decimalFormatSymbols

tiles

fixedTiles

minError

maxError

error

Constructor Detail

TileConfiguration

Method Detail

getTiles

getFixedTiles

getMinError

getMaxError

getError

println

clear

addTile

addTiles

addTiles

fixTile

apply

updateErrors

update

optimizeSilently

optimizeSilently

optimizeSilentlyConcurrent

optimize

optimize

optimize

optimizeAndFilter

optimizeAndFilter

preAlign

getConnectingPointMatches