bunwarpj
Class FinalAction

java.lang.Object
  bunwarpj.FinalAction

All Implemented Interfaces:

java.lang.Runnable

public class FinalAction
extends java.lang.Object
implements java.lang.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.

Field Summary

private int	accurate_mode level of accuracy
private double	consistencyWeight weight for the deformations consistency
private double	curlWeight curl weight
private MainDialog	dialog dialog for bUnwarpJ interface
private double	divWeight divergence weight
private double	imageWeight weight for image similarity
private double	landmarkWeight landmark weight
private int	max_scale_deformation maximum scale deformation
private int	maxImageSubsamplingFactor image subsampling factor at highest resolution level
private int	min_scale_deformation minimum scale deformation
private int	min_scale_image minimum image scale
private int	outputLevel flag to specify the level of resolution in the output
private boolean	showMarquardtOptim flag to show the optimizer
private BSplineModel	source source image model
private double[][]	sourceAffineMatrix source initial affine matrix
private ij.ImagePlus	sourceImp image representation for the source
private Mask	sourceMsk source image mask
private PointHandler	sourcePh point handler for the landmarks in the source image
private double	stopThreshold stopping threshold
private java.lang.Thread	t thread to run the registration method
private BSplineModel	target target image model
private double[][]	targetAffineMatrix target initial affine matrix
private ij.ImagePlus	targetImp image representation for the target
private Mask	targetMsk target image mask
private PointHandler	targetPh point handler for the landmarks in the target image

Constructor Summary

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

Method Summary

java.lang.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, int maxImageSubsamplingFactor) Pass parameter from MainDialog to FinalAction.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

t

private java.lang.Thread t

thread to run the registration method

dialog

private MainDialog dialog

dialog for bUnwarpJ interface

sourceImp

private ij.ImagePlus sourceImp

image representation for the source

targetImp

private ij.ImagePlus targetImp

image representation for the target

source

private BSplineModel source

source image model

target

private BSplineModel target

target image model

sourcePh

private PointHandler sourcePh

point handler for the landmarks in the source image

targetPh

private PointHandler targetPh

point handler for the landmarks in the target image

sourceMsk

private Mask sourceMsk

source image mask

targetMsk

private Mask targetMsk

target image mask

sourceAffineMatrix

private double[][] sourceAffineMatrix

source initial affine matrix

targetAffineMatrix

private double[][] targetAffineMatrix

target initial affine matrix

min_scale_deformation

private int min_scale_deformation

minimum scale deformation

max_scale_deformation

private int max_scale_deformation

maximum scale deformation

min_scale_image

private int min_scale_image

minimum image scale

outputLevel

private int outputLevel

flag to specify the level of resolution in the output

showMarquardtOptim

private boolean showMarquardtOptim

flag to show the optimizer

divWeight

private double divWeight

divergence weight

curlWeight

private double curlWeight

curl weight

landmarkWeight

private double landmarkWeight

landmark weight

imageWeight

private double imageWeight

weight for image similarity

consistencyWeight

private double consistencyWeight

weight for the deformations consistency

stopThreshold

private double stopThreshold

stopping threshold

accurate_mode

private int accurate_mode

level of accuracy

maxImageSubsamplingFactor

private int maxImageSubsamplingFactor

image subsampling factor at highest resolution level

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 java.lang.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 java.lang.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,
                  int maxImageSubsamplingFactor)

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

maxImageSubsamplingFactor - image subsampling factor at highest resolution level

initializeOutputIPs

public ij.ImagePlus[] initializeOutputIPs()

Initialize output image plus

Returns:

target and source output image plus