LayerZPosition (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.janelia.thickness.trakem2.LayerZPosition

All Implemented Interfaces:

TPlugIn
```
public class LayerZPosition
extends Object
implements TPlugIn
```
Author:

Stephan Saalfeld <saalfelds@janelia.hhmi.org>

Field Summary

Fields
Modifier and Type	Field and Description
`protected static int`	`innerIterations`
`protected static double`	`innerRegularize`
`protected static int`	`iterations`
`protected LayerSet`	`layerset`
`protected static int`	`radius`
`protected static double`	`regularize`
`protected static boolean`	`reorder`
`protected static double`	`scale`
`protected static boolean`	`showMatrix`
`protected static Align.Param`	`siftParam`
`protected static String`	`similarityMethod`
`protected static String[]`	`similarityMethods`

Constructor Summary

Constructors
Constructor and Description

LayerZPosition()

Constructors
Constructor and Description
`LayerZPosition()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`applies(Object ob)` Returns true if this plugin can be applied to an Object like @param ob.
`static ij.process.FloatProcessor`	`calculateNCCSimilarity(List<Layer> layers, Rectangle fov, int r, double s)`
`static ij.process.FloatProcessor`	`calculateSIFTSimilarity(List<Layer> layers, Rectangle fov, int r, Align.Param p)`
`protected static ArrayList<Feature>`	`extract(SIFT ijSIFT, ij.process.ImageProcessor ip)`
`Object`	`invoke(Object... params)` Run the plugin directly.
`void`	`invokeNCC(List<Layer> layers, Rectangle fov)` Run plugin with NCC similarity.
`void`	`invokeSIFT(List<Layer> layers, Rectangle fov)` Run plugin with SIFT consensus similarity.
`static void`	`optimize(List<Layer> layers, ij.process.FloatProcessor matrix, int rad, int iter, double reg, int innerIter, double innerReg, boolean reord)`
`static void`	`runNCC(List<Layer> layers, Rectangle fov, int r, double s, int iter, double reg, int innerIter, double innerReg, boolean reord)` Run thickness estimation for a list of layers using NCC similarity.
`static void`	`runSIFT(List<Layer> layers, Rectangle fov, int r, Align.Param p)`
`boolean`	`setup(Object... params)` Setup with optional parameters (may be null).

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

Field Detail

layerset
```
protected LayerSet layerset
```

radius
```
protected static int radius
```

iterations
```
protected static int iterations
```

regularize
```
protected static double regularize
```

innerIterations
```
protected static int innerIterations
```

innerRegularize

protected static double innerRegularize

reorder
```
protected static boolean reorder
```

scale
```
protected static double scale
```

showMatrix
```
protected static boolean showMatrix
```

siftParam
```
protected static Align.Param siftParam
```

similarityMethods

protected static final String[] similarityMethods

similarityMethod

protected static String similarityMethod

Constructor Detail
- LayerZPosition
```
public LayerZPosition()
```

Method Detail

setup
```
public boolean setup(Object... params)
```
Description copied from interface: TPlugIn

Setup with optional parameters (may be null). Returns true of the setup was successful or not interrupted (like by clicking cancel on a dialog).

Specified by:

setup in interface TPlugIn

optimize

public static void optimize(List<Layer> layers,
                            ij.process.FloatProcessor matrix,
                            int rad,
                            int iter,
                            double reg,
                            int innerIter,
                            double innerReg,
                            boolean reord)
                     throws Exception

Throws:: Exception

calculateNCCSimilarity

public static ij.process.FloatProcessor calculateNCCSimilarity(List<Layer> layers,
                                                               Rectangle fov,
                                                               int r,
                                                               double s)
                                                        throws InterruptedException,
                                                               ExecutionException

Throws:: InterruptedException; ExecutionException

runNCC

public static void runNCC(List<Layer> layers,
                          Rectangle fov,
                          int r,
                          double s,
                          int iter,
                          double reg,
                          int innerIter,
                          double innerReg,
                          boolean reord)
                   throws InterruptedException,
                          ExecutionException

Run thickness estimation for a list of layers using NCC similarity.

Parameters:: layers -; fov -; r -; s -
Throws:: InterruptedException; ExecutionException

invokeNCC

public void invokeNCC(List<Layer> layers,
                      Rectangle fov)
               throws InterruptedException,
                      ExecutionException

Run plugin with NCC similarity.

Parameters:: layers -; fov -
Throws:: InterruptedException; ExecutionException

extract

protected static ArrayList<Feature> extract(SIFT ijSIFT,
                                            ij.process.ImageProcessor ip)

calculateSIFTSimilarity

public static ij.process.FloatProcessor calculateSIFTSimilarity(List<Layer> layers,
                                                                Rectangle fov,
                                                                int r,
                                                                Align.Param p)
                                                         throws InterruptedException,
                                                                ExecutionException

Throws:: InterruptedException; ExecutionException

runSIFT

public static void runSIFT(List<Layer> layers,
                           Rectangle fov,
                           int r,
                           Align.Param p)
                    throws InterruptedException,
                           ExecutionException

Throws:: InterruptedException; ExecutionException

invokeSIFT

public void invokeSIFT(List<Layer> layers,
                       Rectangle fov)
                throws InterruptedException,
                       ExecutionException

Run plugin with SIFT consensus similarity.

Parameters:: layers -; fov -
Throws:: ExecutionException; InterruptedException

invoke
```
public Object invoke(Object... params)
```
Description copied from interface: TPlugIn

Run the plugin directly.

Specified by:

invoke in interface TPlugIn

applies
```
public boolean applies(Object ob)
```
Description copied from interface: TPlugIn

Returns true if this plugin can be applied to an Object like @param ob. This may or may not be a Displayable object.

Specified by:

applies in interface TPlugIn

Class LayerZPosition

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

layerset

radius

iterations

regularize

innerIterations

innerRegularize

reorder

scale

showMatrix

siftParam

similarityMethods

similarityMethod

Constructor Detail

LayerZPosition

Method Detail

setup

optimize

calculateNCCSimilarity

runNCC

invokeNCC

extract

calculateSIFTSimilarity

runSIFT

invokeSIFT

invoke

applies