FinalAction (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bunwarpj.FinalAction

All Implemented Interfaces:

Runnable
```
public class FinalAction
extends Object
implements Runnable
```
Class to launch the registration in bUnwarpJ. This is the class called from the main plugin class after recollecting the registration parameters from the main dialog.

Constructor Summary

Constructors
Constructor and Description

FinalAction(MainDialog dialog)
Start a thread under the control of the main event loop.

Constructors
Constructor and Description
`FinalAction(MainDialog dialog)` Start a thread under the control of the main event loop.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Thread`	`getThread()` Get the thread.
`ij.ImagePlus[]`	`initializeOutputIPs()` Initialize output image plus
`void`	`run()` Perform the registration
`void`	setup(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, BSplineModel source, BSplineModel target, PointHandler sourcePh, PointHandler targetPh, Mask sourceMsk, Mask targetMsk, double[][] sourceAffineMatrix, double[][] targetAffineMatrix, int min_scale_deformation, int max_scale_deformation, int min_scale_image, double divWeight, double curlWeight, double landmarkWeight, double imageWeight, double consistencyWeight, double stopThreshold, int outputLevel, boolean showMarquardtOptim, int accurate_mode) Pass parameter from `MainDialog` to `FinalAction`.

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

- Constructor Detail
  - FinalAction
```
public FinalAction(MainDialog dialog)
```
    Start a thread under the control of the main event loop. This thread has access to the progress bar, while methods called directly from within MainDialog do not because they are under the control of its own event loop.
- Method Detail
  - getThread
```
public Thread getThread()
```
    Get the thread.
    
    Returns:
    
    the thread associated with this FinalAction object
  - run
```
public void run()
```
    Perform the registration
    
    Specified by:
    
    run in interface Runnable
  - setup
```
public void setup(ij.ImagePlus sourceImp,
                  ij.ImagePlus targetImp,
                  BSplineModel source,
                  BSplineModel target,
                  PointHandler sourcePh,
                  PointHandler targetPh,
                  Mask sourceMsk,
                  Mask targetMsk,
                  double[][] sourceAffineMatrix,
                  double[][] targetAffineMatrix,
                  int min_scale_deformation,
                  int max_scale_deformation,
                  int min_scale_image,
                  double divWeight,
                  double curlWeight,
                  double landmarkWeight,
                  double imageWeight,
                  double consistencyWeight,
                  double stopThreshold,
                  int outputLevel,
                  boolean showMarquardtOptim,
                  int accurate_mode)
```
    Pass parameter from MainDialog to FinalAction.
    
    Parameters:
    
    sourceImp - image representation for the source
    
    targetImp - image representation for the target
    
    source - source image model
    
    target - target image model
    
    sourcePh - point handler for the landmarks in the source image
    
    targetPh - point handler for the landmarks in the target image
    
    sourceMsk - source image mask
    
    targetMsk - target image mask
    
    sourceAffineMatrix - source initial affine matrix
    
    targetAffineMatrix - target initial affine matrix
    
    min_scale_deformation - minimum scale deformation
    
    max_scale_deformation - maximum scale deformation
    
    min_scale_image - minimum image scale
    
    outputLevel - flag to specify the level of resolution in the output
    
    showMarquardtOptim - flag to show the optimizer
    
    divWeight - divergence weight
    
    curlWeight - curl weight
    
    landmarkWeight - landmark weight
    
    imageWeight - weight for image similarity
    
    consistencyWeight - weight for the deformations consistency
    
    stopThreshold - stopping threshold
    
    accurate_mode - level of accuracy
  - initializeOutputIPs
```
public ij.ImagePlus[] initializeOutputIPs()
```
    Initialize output image plus
    
    Returns:
    
    target and source output image plus

Class FinalAction

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FinalAction

Method Detail

getThread

run

setup

initializeOutputIPs