bunwarpj

Class FinalAction

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.

Method Summary

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