bunwarpj
Class Transformation

java.lang.Object
  bunwarpj.Transformation

public class Transformation
extends java.lang.Object

Class to perform the transformation for bUnwarpJ:

• It stores the information about the bidirectional or unidirectional registration.
• It produces the registration results and the corresponding output if called from dialog.
• The main registration methods are doRegistration (bidirectional) and doUnidirectionalRegistration (unidirectional).
• The intermediate states of the registration are displayed in separate windows (depending on the value of outputLevel.

Nested Class Summary

private class	Transformation.ColorResultTileMaker Class to run concurrent tile windows for final results (color)
private class	Transformation.ConcurrentDeformation Class to concurrently calculate the two deformation mapping tables
private class	Transformation.EvaluateConsistencyTile Class to run concurrent consistency evaluation
private class	Transformation.EvaluateSimilarityTile Class to run concurrent similarity evaluation
private class	Transformation.GrayscaleResultTileMaker Class to run concurrent tile windows for final results (grayscale)
private class	Transformation.OutputTileMaker Class to run concurrent tile windows updaters (for intermediate results)

Field Summary

private int	accurate_mode level of accuracy
private double	consistencyWeight weight for the deformations consistency
private double	curlWeight curl weight
private double[][]	cxSourceToTarget x- B-spline coefficients keeping the transformation from source to target
private double[][]	cxTargetToSource x- B-spline coefficients keeping the transformation from target to source
private double[][]	cySourceToTarget y- B-spline coefficients keeping the transformation from source to target
private double[][]	cyTargetToSource y- B-spline coefficients keeping the transformation from target to source
private MainDialog	dialog pointer to the dialog of the bUnwarpJ interface
private double	divWeight divergence weight
private double	finalDirectConsistencyError direct consistency error at the end of the registration
private double	finalDirectLandmarkError direct landmarks error at the end of the registration
private double	finalDirectRegularizationError direct regularization error at the end of the registration
private double	finalDirectSimilarityError direct similarity error at the end of the registration
private double	finalInverseConsistencyError inverse consistency error at the end of the registration
private double	finalInverseLandmarkError inverse landmarks error at the end of the registration
private double	finalInverseRegularizationError inverse regularization error at the end of the registration
private double	finalInverseSimilarityError inverse similarity error at the end of the registration
private double	FLT_EPSILON float epsilon
private java.lang.String	fn_tnf_1 direct transformation file name
private java.lang.String	fn_tnf_2 inverse transformation file name
private double	imageWeight weight for image similarity
private int	intervals number of intervals to place B-spline coefficients
private double	landmarkWeight landmark weight
private int	max_scale_deformation maximum scale deformation
private int	min_scale_deformation minimum scale deformation
private int	min_scale_image minimum scale image
private boolean	ORIGINAL original flag
private ij.process.ImageProcessor	originalSourceIP initial source image processor
private ij.process.ImageProcessor	originalTargetIP initial target image processor
private ij.ImagePlus	output_ip_1 reference to the first output image
private ij.ImagePlus	output_ip_2 reference to the second output image
private int	outputLevel flag to specify the level of resolution in the output
private double[][]	P11_SourceToTarget regularization P11 (source to target) matrix
private double[][]	P11_TargetToSource regularization P11 (target to source) matrix
private double[][]	P12_SourceToTarget regularization P12 (source to target) matrix
private double[][]	P12_TargetToSource regularization P12 (target to source) matrix
private double[][]	P22_SourceToTarget regularization P22 (source to target) matrix
private double[][]	P22_TargetToSource regularization P22 (target to source) matrix
private double	partialDirectConsitencyError direct consistency error for the current iteration
private double	partialDirectLandmarkError direct landmarks error for the current iteration
private double	partialDirectRegularizationError direct regularization error for the current iteration
private double	partialDirectSimilarityError direct similarity error for the current iteration
private double	partialInverseConsitencyError inverse consistency error for the current iteration
private double	partialInverseLandmarkError inverse landmarks error for the current iteration
private double	partialInverseRegularizationError inverse regularization error for the current iteration
private double	partialInverseSimilarityError inverse similarity error for the current iteration
private boolean	PYRAMID pyramid flag
private boolean	showMarquardtOptim flag to show the optimizer
private BSplineModel	source pointer to the source image model
private double[][]	sourceAffineMatrix initial affine matrix for the source image
private int	sourceCurrentHeight source image current height
private int	sourceCurrentWidth source image current width
private double	sourceFactorHeight height factor in the source image
private double	sourceFactorWidth width factor in the source image
private int	sourceHeight source image height
private ij.ImagePlus	sourceImp pointer to the source image representation
private Mask	sourceMsk pointer to the source mask
private PointHandler	sourcePh pointer to the source point handler
private int	sourceWidth source image width
private double	stopThreshold stopping threshold
private BSplineModel	swxSourceToTarget image model to interpolate the cxSourceToTarget coefficients
private BSplineModel	swxTargetToSource image model to interpolate the cxTargetToSource coefficients
private BSplineModel	swySourceToTarget image model to interpolate the cySourceToTarget coefficients
private BSplineModel	swyTargetToSource image model to interpolate the cyTargetToSource coefficients
private BSplineModel	target pointer to the target image model
private double[][]	targetAffineMatrix initial affine matrix for the target image
private int	targetCurrentHeight target image current height
private int	targetCurrentWidth target image current width
private double	targetFactorHeight height factor in the target image
private double	targetFactorWidth width factor in the target image
private int	targetHeight target image height
private ij.ImagePlus	targetImp pointer to the target image representation
private Mask	targetMsk pointer to the target mask
private PointHandler	targetPh pointer to the target point handler
private int	targetWidth source image width
private int	transformationSplineDegree degree of the B-splines involved in the transformation

Constructor Summary

Transformation(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, java.lang.String fn_tnf_1, java.lang.String fn_tnf_2, ij.ImagePlus output_ip_1, ij.ImagePlus output_ip_2, MainDialog dialog)
Create an instance of Transformation.

Transformation(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, java.lang.String fn_tnf_1, java.lang.String fn_tnf_2, ij.ImagePlus output_ip_1, ij.ImagePlus output_ip_2, MainDialog dialog, ij.process.ImageProcessor originalSourceIP, ij.process.ImageProcessor originalTargetIP)
Create an instance of Transformation.

Method Summary

private ij.ImagePlus	applyTransformationMultiThread(int intervals, double[][] cx, double[][] cy, boolean bIsReverse) Apply the final transformation (multi-thread version).
private void	build_Matrix_B(int intervals, int K, double[][] B, boolean bIsReverse) Build the matrix for the landmark interpolation.
private double	build_Matrix_R_computeIntegral_aa(double x0, double xF, double s1, double s2, double h, int q1, int q2) Compute the following integral
private double	build_matrix_R_computeIntegral_BB(double x0, double xF, double s1, double s2, double h, int n1, int n2) Compute the following integral
private double	build_matrix_R_computeIntegral_xx(double x0, double xF, double s1, double s2, int q1, int q2)
private void	build_Matrix_R_geteta(double[][] etaq1q2, int q1, int q2, int dim, int intervals) Build matrix R, get eta.
private boolean	build_Matrix_R_getetaindex(int ki1, int ki2, int intervals, int[] ip) Build matrix R, get eta index.
private void	build_Matrix_Rq1q2(int intervals, double weight, int q1, int q2, double[][] R, boolean bIsReverse) Build matrix Rq1q2.
private void	build_Matrix_Rq1q2q3q4(int intervals, double weight, int q1, int q2, int q3, int q4, double[][] R, boolean bIsReverse) Build matrix Rq1q2q3q4.
private void	buildRegularizationTemporary(int intervals, boolean bIsReverse) Build regularization temporary.
private double[][]	computeAffineMatrix(boolean bIsReverse) Compute the affine matrix.
private void	computeAffineResidues(double[][] affineMatrix, double[] dx, double[] dy, boolean bIsReverse) Deprecated.
private boolean	computeCoefficientsScale(int intervals, double[] dx, double[] dy, double[][] cx, double[][] cy, boolean bIsReverse) Compute the coefficients at this scale.
private boolean	computeCoefficientsScaleWithRegularization(int intervals, double[] dx, double[] dy, double[][] cx, double[][] cy, boolean bIsReverse) Compute the coefficients scale with regularization.
private void	computeDeformation(int intervals, double[][] cx, double[][] cy, double[][] transformation_x, double[][] transformation_y, boolean bIsReverse) Compute the deformation.
private void	computeDeformationGrid(int intervals, double[][] cx, double[][] cy, ij.ImageStack is, boolean bIsReverse) Compute and draw the final deformation grid.
private void	computeDeformationVectors(int intervals, double[][] cx, double[][] cy, ij.ImageStack is, boolean bIsReverse) Compute and draw the final deformation vectors.
private void	computeInitialResidues(double[] dx, double[] dy, boolean bIsReverse) Deprecated.
private double[][]	computeRotationMatrix(boolean bIsReverse) Compute the rotation matrix.
private void	computeScaleResidues(int intervals, double[][] cx, double[][] cy, double[] dx, double[] dy, boolean bIsReverse) Deprecated.
private void	computeTotalWorkload() This code is an excerpt from doRegistration() to compute the exact number of steps.
void	doRegistration() Registration method.
void	doUnidirectionalRegistration() Unidirectional registration method.
private double	energyFunction(double[] c, int intervals, double[] grad, boolean only_image, boolean show_error) Energy function to be minimized by the optimizer in the bidirectional case.
private double	evaluateConsistency(double[] c_direct, double[] c_inverse, int intervals, double[] grad) Deprecated.
private double	evaluateConsistency(int intervals, double[] grad) Deprecated.
private double	evaluateConsistencyMultiThread(int intervals, double[] grad) Calculate the geometric error between the source-target and target-source deformations.
double	evaluateImageSimilarity(boolean bIsReverse) Evaluate the similarity between the images.
private double	evaluatePartialEnergy(double[] c, int intervals, double[] grad_direct, double[] grad_inverse, boolean only_image, boolean show_error, boolean bIsReverse) Evaluate the energy function in one direction (direct or inverse) and calculates its gradient.
private double	evaluateSimilarity(double[] c, int intervals, double[] grad, boolean only_image, boolean show_error, boolean bIsReverse) Deprecated.
private double	evaluateSimilarityMultiThread(double[] c, int intervals, double[] grad, boolean only_image, boolean bIsReverse) Evaluate the similarity between the source and the target images but also the transformation regularization and and landmarks energy term if necessary.
void	getDeformation(double[][] transformation_x, double[][] transformation_y, boolean bIsReverse) Get the deformation from the corresponding coefficients.
double[][]	getDirectDeformationCoefficientsX() Get the direct deformation X coefficients.
double[][]	getDirectDeformationCoefficientsY() Get the direct deformation Y coefficients.
ij.ImagePlus	getDirectResults() Get direct results window
int	getIntervals() Get the current number of intervals between B-spline coefficients.
double[][]	getInverseDeformationCoefficientsX() Get the inverse deformation X coefficients.
double[][]	getInverseDeformationCoefficientsY() Get the inverse deformation Y coefficients.
ij.ImagePlus	getInverseResults() Get inverse results window
private void	Marquardt_it(double[] x, boolean[] optimize, double[] gradient, double[] Hessian, double lambda) In this function the system (H+lambda*Diag(H))*update=gradient is solved for update.
private double	optimizeCoeffs(int intervals, double thChangef, double[][] cxTargetToSource, double[][] cyTargetToSource) Optimize the B-spline coefficients (unidirectional method).
private double	optimizeCoeffs(int intervals, double thChangef, double[][] cxTargetToSource, double[][] cyTargetToSource, double[][] cxSourceToTarget, double[][] cySourceToTarget) Optimize the B-spline coefficients (bidirectional method).
private double[][]	propagateCoeffsToNextLevel(int intervals, double[][] c, double expansionFactor) Propagate deformation coefficients to the next level.
void	saveDirectTransformation() Save source transformation.
void	saveInverseTransformation() Save target transformation.
private void	saveTransformation(int intervals, double[][] cx, double[][] cy, boolean bIsReverse) Save the transformation.
void	showDirectResults() Show the direct transformation results(multi-thread version).
void	showInverseResults() Show the inverse transformation results (multi-thread version).
private void	showTransformation(int intervals, double[][] cx, double[][] cy, boolean bIsReverse) Deprecated.
private void	showTransformationMultiThread(int intervals, double[][] cx, double[][] cy, boolean bIsReverse) Show the transformation (multi-thread version).
void	transform(double u, double v, double[] xyF, boolean bIsReverse) Apply the current transformation to a given point.
private void	update_current_output(double[] c, int intervals, boolean bIsReverse) Method to update a current output (multi-thread).
private void	update_outputs(double[] c, int intervals) Method to update both current outputs (source-target and target-source).
private double[]	xWeight(double x, int xIntervals, boolean extended, boolean bIsReverse) Calculate the cubic B-spline x weight.
private double[]	yWeight(double y, int yIntervals, boolean extended, boolean bIsReverse) Calculate the cubic B-spline y weight.

Methods inherited from class java.lang.Object

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

Field Detail

FLT_EPSILON

private final double FLT_EPSILON

float epsilon

PYRAMID

private final boolean PYRAMID

pyramid flag

See Also:

Constant Field Values

ORIGINAL

private final boolean ORIGINAL

original flag

See Also:

Constant Field Values

transformationSplineDegree

private final int transformationSplineDegree

degree of the B-splines involved in the transformation

See Also:

Constant Field Values

output_ip_1

private ij.ImagePlus output_ip_1

reference to the first output image

output_ip_2

private ij.ImagePlus output_ip_2

reference to the second output image

dialog

private MainDialog dialog

pointer to the dialog of the bUnwarpJ interface

sourceImp

private ij.ImagePlus sourceImp

pointer to the source image representation

targetImp

private ij.ImagePlus targetImp

pointer to the target image representation

source

private BSplineModel source

pointer to the source image model

target

private BSplineModel target

pointer to the target image model

originalSourceIP

private ij.process.ImageProcessor originalSourceIP

initial source image processor

originalTargetIP

private ij.process.ImageProcessor originalTargetIP

initial target image processor

sourcePh

private PointHandler sourcePh

pointer to the source point handler

targetPh

private PointHandler targetPh

pointer to the target point handler

sourceMsk

private Mask sourceMsk

pointer to the source mask

targetMsk

private Mask targetMsk

pointer to the target mask

sourceAffineMatrix

private double[][] sourceAffineMatrix

initial affine matrix for the source image

targetAffineMatrix

private double[][] targetAffineMatrix

initial affine matrix for the target image

sourceHeight

private int sourceHeight

source image height

sourceWidth

private int sourceWidth

source image width

targetHeight

private int targetHeight

target image height

targetWidth

private int targetWidth

source image width

targetCurrentHeight

private int targetCurrentHeight

target image current height

targetCurrentWidth

private int targetCurrentWidth

target image current width

sourceCurrentHeight

private int sourceCurrentHeight

source image current height

sourceCurrentWidth

private int sourceCurrentWidth

source image current width

targetFactorHeight

private double targetFactorHeight

height factor in the target image

targetFactorWidth

private double targetFactorWidth

width factor in the target image

sourceFactorHeight

private double sourceFactorHeight

height factor in the source image

sourceFactorWidth

private double sourceFactorWidth

width factor in the source image

partialDirectSimilarityError

private double partialDirectSimilarityError

direct similarity error for the current iteration

partialDirectRegularizationError

private double partialDirectRegularizationError

direct regularization error for the current iteration

partialDirectLandmarkError

private double partialDirectLandmarkError

direct landmarks error for the current iteration

partialDirectConsitencyError

private double partialDirectConsitencyError

direct consistency error for the current iteration

finalDirectSimilarityError

private double finalDirectSimilarityError

direct similarity error at the end of the registration

finalDirectRegularizationError

private double finalDirectRegularizationError

direct regularization error at the end of the registration

finalDirectLandmarkError

private double finalDirectLandmarkError

direct landmarks error at the end of the registration

finalDirectConsistencyError

private double finalDirectConsistencyError

direct consistency error at the end of the registration

partialInverseSimilarityError

private double partialInverseSimilarityError

inverse similarity error for the current iteration

partialInverseRegularizationError

private double partialInverseRegularizationError

inverse regularization error for the current iteration

partialInverseLandmarkError

private double partialInverseLandmarkError

inverse landmarks error for the current iteration

partialInverseConsitencyError

private double partialInverseConsitencyError

inverse consistency error for the current iteration

finalInverseSimilarityError

private double finalInverseSimilarityError

inverse similarity error at the end of the registration

finalInverseRegularizationError

private double finalInverseRegularizationError

inverse regularization error at the end of the registration

finalInverseLandmarkError

private double finalInverseLandmarkError

inverse landmarks error at the end of the registration

finalInverseConsistencyError

private double finalInverseConsistencyError

inverse consistency error at the end of the registration

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 scale image

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

fn_tnf_1

private java.lang.String fn_tnf_1

direct transformation file name

fn_tnf_2

private java.lang.String fn_tnf_2

inverse transformation file name

intervals

private int intervals

number of intervals to place B-spline coefficients

cxSourceToTarget

private double[][] cxSourceToTarget

x- B-spline coefficients keeping the transformation from source to target

cySourceToTarget

private double[][] cySourceToTarget

y- B-spline coefficients keeping the transformation from source to target

cxTargetToSource

private double[][] cxTargetToSource

x- B-spline coefficients keeping the transformation from target to source

cyTargetToSource

private double[][] cyTargetToSource

y- B-spline coefficients keeping the transformation from target to source

swxSourceToTarget

private BSplineModel swxSourceToTarget

image model to interpolate the cxSourceToTarget coefficients

swySourceToTarget

private BSplineModel swySourceToTarget

image model to interpolate the cySourceToTarget coefficients

swxTargetToSource

private BSplineModel swxTargetToSource

image model to interpolate the cxTargetToSource coefficients

swyTargetToSource

private BSplineModel swyTargetToSource

image model to interpolate the cyTargetToSource coefficients

P11_SourceToTarget

private double[][] P11_SourceToTarget

regularization P11 (source to target) matrix

P22_SourceToTarget

private double[][] P22_SourceToTarget

regularization P22 (source to target) matrix

P12_SourceToTarget

private double[][] P12_SourceToTarget

regularization P12 (source to target) matrix

P11_TargetToSource

private double[][] P11_TargetToSource

regularization P11 (target to source) matrix

P22_TargetToSource

private double[][] P22_TargetToSource

regularization P22 (target to source) matrix

P12_TargetToSource

private double[][] P12_TargetToSource

regularization P12 (target to source) matrix

Constructor Detail

Transformation

public Transformation(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,
                      java.lang.String fn_tnf_1,
                      java.lang.String fn_tnf_2,
                      ij.ImagePlus output_ip_1,
                      ij.ImagePlus output_ip_2,
                      MainDialog dialog)

Create an instance of Transformation.

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 - source initial affine matrix

min_scale_deformation - minimum scale deformation

max_scale_deformation - maximum scale deformation

min_scale_image - minimum image scale

divWeight - divergence weight

curlWeight - curl weight

landmarkWeight - landmark weight

imageWeight - weight for image similarity

consistencyWeight - weight for the deformations consistency

stopThreshold - stopping threshold

outputLevel - flag to specify the level of resolution in the output

showMarquardtOptim - flag to show the optimizer

accurate_mode - level of accuracy

fn_tnf_1 - direct transformation file name

fn_tnf_2 - inverse transformation file name

output_ip_1 - pointer to the first output image

output_ip_2 - pointer to the second output image

dialog - pointer to the dialog of the bUnwarpJ interface

Transformation

public Transformation(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,
                      java.lang.String fn_tnf_1,
                      java.lang.String fn_tnf_2,
                      ij.ImagePlus output_ip_1,
                      ij.ImagePlus output_ip_2,
                      MainDialog dialog,
                      ij.process.ImageProcessor originalSourceIP,
                      ij.process.ImageProcessor originalTargetIP)

Create an instance of Transformation.

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 - source initial affine matrix

min_scale_deformation - minimum scale deformation

max_scale_deformation - maximum scale deformation

min_scale_image - minimum image scale

divWeight - divergence weight

curlWeight - curl weight

landmarkWeight - landmark weight

imageWeight - weight for image similarity

consistencyWeight - weight for the deformations consistency

stopThreshold - stopping threshold

outputLevel - flag to specify the level of resolution in the output

showMarquardtOptim - flag to show the optimizer

accurate_mode - level of accuracy

fn_tnf_1 - direct transformation file name

fn_tnf_2 - inverse transformation file name

output_ip_1 - pointer to the first output image

output_ip_2 - pointer to the second output image

dialog - pointer to the dialog of the bUnwarpJ interface

Method Detail

doRegistration

public void doRegistration()

Registration method. It applies the consistent and elastic registration algorithm to the selected source and target images.

doUnidirectionalRegistration

public void doUnidirectionalRegistration()

Unidirectional registration method. It applies unidirectional elastic registration to the selected source and target images.

evaluateImageSimilarity

public double evaluateImageSimilarity(boolean bIsReverse)

Evaluate the similarity between the images.

Parameters:

bIsReverse - determines the transformation direction (source-target=TRUE or target-source=FALSE)

Returns:

image similarity value

getDeformation

public void getDeformation(double[][] transformation_x,
                           double[][] transformation_y,
                           boolean bIsReverse)

Get the deformation from the corresponding coefficients.

Parameters:

transformation_x - matrix to store the x- transformation

transformation_y - matrix to store the y- transformation

bIsReverse - flag to choose the deformation coefficients (source-target=TRUE or target-source=FALSE)

getDirectDeformationCoefficientsX

public double[][] getDirectDeformationCoefficientsX()

Get the direct deformation X coefficients.

Returns:

coefficients array

getDirectDeformationCoefficientsY

public double[][] getDirectDeformationCoefficientsY()

Get the direct deformation Y coefficients.

Returns:

coefficients array

getInverseDeformationCoefficientsX

public double[][] getInverseDeformationCoefficientsX()

Get the inverse deformation X coefficients.

Returns:

coefficients array

getInverseDeformationCoefficientsY

public double[][] getInverseDeformationCoefficientsY()

Get the inverse deformation Y coefficients.

Returns:

coefficients array

getIntervals

public int getIntervals()

Get the current number of intervals between B-spline coefficients.

Returns:

coefficients array

transform

public void transform(double u,
                      double v,
                      double[] xyF,
                      boolean bIsReverse)

Apply the current transformation to a given point.

Parameters:

u - input, x- point coordinate

v - input, y- point coordinate

xyF - output, transformed point

bIsReverse - flag to decide the transformation direction (direct-inverse) (source-target=TRUE or target-source=FALSE)

build_Matrix_B

private void build_Matrix_B(int intervals,
                            int K,
                            double[][] B,
                            boolean bIsReverse)

Build the matrix for the landmark interpolation.

Parameters:

intervals - Intervals in the deformation

K - Number of landmarks

B - System matrix of the landmark interpolation

bIsReverse - determines the transformation direction (source-target=TRUE or target-source=FALSE)

build_Matrix_Rq1q2

private void build_Matrix_Rq1q2(int intervals,
                                double weight,
                                int q1,
                                int q2,
                                double[][] R,
                                boolean bIsReverse)

Build matrix Rq1q2.

build_Matrix_Rq1q2q3q4

private void build_Matrix_Rq1q2q3q4(int intervals,
                                    double weight,
                                    int q1,
                                    int q2,
                                    int q3,
                                    int q4,
                                    double[][] R,
                                    boolean bIsReverse)

Build matrix Rq1q2q3q4.

build_Matrix_R_computeIntegral_aa

private double build_Matrix_R_computeIntegral_aa(double x0,
                                                 double xF,
                                                 double s1,
                                                 double s2,
                                                 double h,
                                                 int q1,
                                                 int q2)

Compute the following integral

           xF d^q1      3  x        d^q2    3  x
  integral    -----   B  (--- - s1) ----- B  (--- - s2) dx
           x0 dx^q1        h        dx^q2      h

build_matrix_R_computeIntegral_BB

private double build_matrix_R_computeIntegral_BB(double x0,
                                                 double xF,
                                                 double s1,
                                                 double s2,
                                                 double h,
                                                 int n1,
                                                 int n2)

Compute the following integral

           xF   n1  x          n2  x
  integral     B  (--- - s1)  B  (--- - s2) dx
           x0       h              h

build_matrix_R_computeIntegral_xx

private double build_matrix_R_computeIntegral_xx(double x0,
                                                 double xF,
                                                 double s1,
                                                 double s2,
                                                 int q1,
                                                 int q2)

 Computation of the integral:
             xF          q1       q2
    integral       (x-s1)   (x-s2)     dx
             x0          +        +

build_Matrix_R_geteta

private void build_Matrix_R_geteta(double[][] etaq1q2,
                                   int q1,
                                   int q2,
                                   int dim,
                                   int intervals)

Build matrix R, get eta.

build_Matrix_R_getetaindex

private boolean build_Matrix_R_getetaindex(int ki1,
                                           int ki2,
                                           int intervals,
                                           int[] ip)

Build matrix R, get eta index.

buildRegularizationTemporary

private void buildRegularizationTemporary(int intervals,
                                          boolean bIsReverse)

Build regularization temporary.

Parameters:

intervals - intervals in the deformation

bIsReverse - determines the transformation direction (source-target=TRUE or target-source=FALSE)

computeAffineMatrix

private double[][] computeAffineMatrix(boolean bIsReverse)

Compute the affine matrix.

Parameters:

bIsReverse - determines the transformation direction (source-target=TRUE or target-source=FALSE)

computeAffineResidues

private void computeAffineResidues(double[][] affineMatrix,
                                   double[] dx,
                                   double[] dy,
                                   boolean bIsReverse)

Deprecated.

Compute the affine residues for the landmarks.

NOTE: The output vectors should be already resized

Parameters:

affineMatrix - Input

dx - Output, difference in x for each landmark

dy - Output, difference in y for each landmark

bIsReverse - determines the transformation direction (source-target=TRUE or target-source=FALSE)

computeCoefficientsScale

private boolean computeCoefficientsScale(int intervals,
                                         double[] dx,
                                         double[] dy,
                                         double[][] cx,
                                         double[][] cy,
                                         boolean bIsReverse)

Compute the coefficients at this scale.

Parameters:

intervals - input, number of intervals at this scale

dx - input, x residue so far

dy - input, y residue so far

cx - output, x coefficients for splines

cy - output, y coefficients for splines

bIsReverse - determines the transformation direction (source-target=TRUE or target-source=FALSE)

Returns:

under-constrained flag

computeCoefficientsScaleWithRegularization

private boolean computeCoefficientsScaleWithRegularization(int intervals,
                                                           double[] dx,
                                                           double[] dy,
                                                           double[][] cx,
                                                           double[][] cy,
                                                           boolean bIsReverse)

Compute the coefficients scale with regularization.

Parameters:

intervals - input, number of intervals at this scale

dx - input, x residue so far

dy - input, y residue so far

cx - output, x coefficients for splines

cy - output, y coefficients for splines

bIsReverse - determines the transformation direction (source-target=TRUE or target-source=FALSE)

Returns:

under-constrained flag

computeInitialResidues

private void computeInitialResidues(double[] dx,
                                    double[] dy,
                                    boolean bIsReverse)

Deprecated.

Compute the initial residues for the landmarks.

NOTE: The output vectors should be already resized

Parameters:

dx - output, difference in x for each landmark

dy - output, difference in y for each landmark

bIsReverse - determines the transformation direction (source-target=TRUE or target-source=FALSE)

computeDeformation

private void computeDeformation(int intervals,
                                double[][] cx,
                                double[][] cy,
                                double[][] transformation_x,
                                double[][] transformation_y,
                                boolean bIsReverse)

Compute the deformation.

Parameters:

intervals - input, number of intervals

cx - input, X B-spline coefficients

cy - input, Y B-spline coefficients

transformation_x - output, X transformation map

transformation_y - output, Y transformation map

bIsReverse - determines the transformation direction (source-target=TRUE or target-source=FALSE)

computeRotationMatrix

private double[][] computeRotationMatrix(boolean bIsReverse)

Compute the rotation matrix.

Parameters:

bIsReverse - determines the transformation direction (source-target=TRUE or target-source=FALSE)

Returns:

rotation matrix

computeScaleResidues

private void computeScaleResidues(int intervals,
                                  double[][] cx,
                                  double[][] cy,
                                  double[] dx,
                                  double[] dy,
                                  boolean bIsReverse)

Deprecated.

Compute the scale residues.

NOTE: At the input dx and dy have the residues so far, at the output these residues are modified to account for the model at the new scale

Parameters:

intervals - input, number of intervals

cx - input, X B-spline coefficients

cy - input, Y B-spline coefficients

dx - input/output, X residues

dy - input/output, Y residues

bIsReverse - determines the transformation direction (target-source=FALSE or source-target=TRUE)

computeTotalWorkload

private void computeTotalWorkload()

This code is an excerpt from doRegistration() to compute the exact number of steps.

evaluateConsistency

private double evaluateConsistency(int intervals,
                                   double[] grad)

Deprecated.

Calculate the geometric error between the source-target and target-source deformations (the corresponding coefficients are assumed to be at swxTargetToSource, swyTargetToSource, swxSourceToTarget and swySourceToTarget).

Parameters:

intervals - Input: Number of intervals for the deformation

grad - Output: Gradient of the function

Returns:

geometric error between the source-target and target-source deformations.

evaluateConsistency

private double evaluateConsistency(double[] c_direct,
                                   double[] c_inverse,
                                   int intervals,
                                   double[] grad)

Deprecated.

Calculate the geometric error between the source-target and target-source deformations.

Parameters:

c_direct - Input: Direct deformation coefficients

c_inverse - Input: Inverse deformation coefficients

intervals - Input: Number of intervals for the deformation

grad - Output: Gradient of the function

Returns:

error function value

energyFunction

private double energyFunction(double[] c,
                              int intervals,
                              double[] grad,
                              boolean only_image,
                              boolean show_error)

Energy function to be minimized by the optimizer in the bidirectional case.

Parameters:

c - Input: Deformation coefficients

intervals - Input: Number of intervals for the deformation

grad - Output: Gradient of the function

only_image - Input: if true, only the image term is considered and not the regularization

show_error - Input: if true, an image is shown with the error

Returns:

value of the energy function for these deformation coefficients

evaluateSimilarity

private double evaluateSimilarity(double[] c,
                                  int intervals,
                                  double[] grad,
                                  boolean only_image,
                                  boolean show_error,
                                  boolean bIsReverse)

Deprecated.

Evaluate the similarity between the source and the target images but also the transformation regularization and and landmarks energy term if necessary.

Parameters:

c - Input: Deformation coefficients

intervals - Input: Number of intervals for the deformation

grad - Output: Gradient of the similarity

only_image - Input: if true, only the image term is considered and not the regularization

show_error - Input: if true, an image is shown with the error

bIsReverse - Input: flag to determine the transformation direction (target-source=FALSE or source-target=TRUE)

Returns:

images similarity value

evaluatePartialEnergy

private double evaluatePartialEnergy(double[] c,
                                     int intervals,
                                     double[] grad_direct,
                                     double[] grad_inverse,
                                     boolean only_image,
                                     boolean show_error,
                                     boolean bIsReverse)

Evaluate the energy function in one direction (direct or inverse) and calculates its gradient.

Energy function:

E = w_i * E_similarity + w_l * E_landmarks + (w_r * E_rotational + w_d * E_divergence) + w_c * E_consistency

Parameters:

c - Input: Deformation coefficients

intervals - Input: Number of intervals for the deformation

grad_direct - Output: Gradient of the energy function (direct direction)

grad_inverse - Output: Gradient of the energy function (inverse direction)

only_image - Input: if true, only the image term is considered and not the regularization

show_error - Input: if true, an image is shown with the error

bIsReverse - Input: flag to determine the transformation direction (target-source=FALSE or source-target=TRUE)

Returns:

images similarity value

Marquardt_it

private void Marquardt_it(double[] x,
                          boolean[] optimize,
                          double[] gradient,
                          double[] Hessian,
                          double lambda)

In this function the system (H+lambda*Diag(H))*update=gradient is solved for update. H is the hessian of the function f, gradient is the gradient of the function f, Diag(H) is a matrix with the diagonal of H.

optimizeCoeffs

private double optimizeCoeffs(int intervals,
                              double thChangef,
                              double[][] cxTargetToSource,
                              double[][] cyTargetToSource,
                              double[][] cxSourceToTarget,
                              double[][] cySourceToTarget)

Optimize the B-spline coefficients (bidirectional method).

Parameters:

intervals - number of intervals in the deformation

thChangef -

cxTargetToSource - x- B-spline coefficients storing the target to source deformation

cyTargetToSource - y- B-spline coefficients storing the target to source deformation

cxSourceToTarget - x- B-spline coefficients storing the source to target deformation

cySourceToTarget - y- B-spline coefficients storing the source to target deformation

Returns:

energy function value

optimizeCoeffs

private double optimizeCoeffs(int intervals,
                              double thChangef,
                              double[][] cxTargetToSource,
                              double[][] cyTargetToSource)

Optimize the B-spline coefficients (unidirectional method).

Parameters:

intervals - number of intervals in the deformation

thChangef -

cxTargetToSource - x- B-spline coefficients storing the target to source deformation

cyTargetToSource - y- B-spline coefficients storing the target to source deformation

Returns:

energy function value

propagateCoeffsToNextLevel

private double[][] propagateCoeffsToNextLevel(int intervals,
                                              double[][] c,
                                              double expansionFactor)

Propagate deformation coefficients to the next level.

Parameters:

intervals - number of intervals in the deformation

c - B-spline coefficients

expansionFactor - due to the change of size in the represented image

Returns:

propagated coefficients

saveDirectTransformation

public void saveDirectTransformation()

Save source transformation. GUI mode.

saveInverseTransformation

public void saveInverseTransformation()

Save target transformation. GUI mode.

saveTransformation

private void saveTransformation(int intervals,
                                double[][] cx,
                                double[][] cy,
                                boolean bIsReverse)

Save the transformation.

Parameters:

intervals - number of intervals in the deformation

cx - x- deformation coefficients

cy - y- deformation coefficients

bIsReverse - flat to determine the transformation direction

computeDeformationGrid

private void computeDeformationGrid(int intervals,
                                    double[][] cx,
                                    double[][] cy,
                                    ij.ImageStack is,
                                    boolean bIsReverse)

Compute and draw the final deformation grid.

Parameters:

intervals - number of intervals in the deformation

cx - x- deformation coefficients

cy - y- deformation coefficients

is - image stack where we want to show the deformation grid

bIsReverse - flag to determine the transformation direction (target-source=FALSE or source-target=TRUE)

computeDeformationVectors

private void computeDeformationVectors(int intervals,
                                       double[][] cx,
                                       double[][] cy,
                                       ij.ImageStack is,
                                       boolean bIsReverse)

Compute and draw the final deformation vectors.

Parameters:

intervals - number of intervals in the deformation

cx - x- deformation coefficients

cy - y- deformation coefficients

is - image stack where we want to show the deformation vectors

bIsReverse - flag to determine the transformation direction (target-source=FALSE or source-target=TRUE)

showDirectResults

public void showDirectResults()

Show the direct transformation results(multi-thread version).

showInverseResults

public void showInverseResults()

Show the inverse transformation results (multi-thread version).

showTransformationMultiThread

private void showTransformationMultiThread(int intervals,
                                           double[][] cx,
                                           double[][] cy,
                                           boolean bIsReverse)

Show the transformation (multi-thread version).

Parameters:

intervals - number of intervals in the deformation

cx - x- deformation coefficients

cy - y- deformation coefficients

bIsReverse - flag to determine the transformation direction (target-source=FALSE or source-target=TRUE)

getDirectResults

public ij.ImagePlus getDirectResults()

Get direct results window

Returns:

direct registration results

getInverseResults

public ij.ImagePlus getInverseResults()

Get inverse results window

Returns:

inverse registration results

applyTransformationMultiThread

private ij.ImagePlus applyTransformationMultiThread(int intervals,
                                                    double[][] cx,
                                                    double[][] cy,
                                                    boolean bIsReverse)

Apply the final transformation (multi-thread version).

Parameters:

intervals - number of intervals in the deformation

cx - x- deformation coefficients

cy - y- deformation coefficients

bIsReverse - flag to determine the transformation direction (target-source=FALSE or source-target=TRUE)

Returns:

output images (depending on the output level)

showTransformation

private void showTransformation(int intervals,
                                double[][] cx,
                                double[][] cy,
                                boolean bIsReverse)

Deprecated.

Show the transformation (calculating entire transformation tables).

Parameters:

intervals - number of intervals in the deformation

cx - x- deformation coefficients

cy - y- deformation coefficients

bIsReverse - flag to determine the transformation direction (target-source=FALSE or source-target=TRUE)

update_outputs

private void update_outputs(double[] c,
                            int intervals)

Method to update both current outputs (source-target and target-source).

Parameters:

c - B-spline coefficients

intervals - number of intervals in the deformation

update_current_output

private void update_current_output(double[] c,
                                   int intervals,
                                   boolean bIsReverse)

Method to update a current output (multi-thread).

Parameters:

c - B-spline coefficients

intervals - number of intervals in the deformation

bIsReverse - flag to decide the deformation direction (source-target, target-source)

xWeight

private double[] xWeight(double x,
                         int xIntervals,
                         boolean extended,
                         boolean bIsReverse)

Calculate the cubic B-spline x weight.

Parameters:

x - x- value

xIntervals - x- number of intervals

extended - extended flat

bIsReverse - flag to determine the transformation direction (target-source=FALSE or source-target=TRUE)

Returns:

weights

yWeight

private double[] yWeight(double y,
                         int yIntervals,
                         boolean extended,
                         boolean bIsReverse)

Calculate the cubic B-spline y weight.

Parameters:

y - y- value

yIntervals - y- number of intervals

extended - extended flat

bIsReverse - flag to determine the transformation direction (target-source=FALSE or source-target=TRUE)

Returns:

weights

evaluateSimilarityMultiThread

private double evaluateSimilarityMultiThread(double[] c,
                                             int intervals,
                                             double[] grad,
                                             boolean only_image,
                                             boolean bIsReverse)

Evaluate the similarity between the source and the target images but also the transformation regularization and and landmarks energy term if necessary. Multi-threading version.

Parameters:

c - Input: Deformation coefficients

intervals - Input: Number of intervals for the deformation

grad - Output: Gradient of the similarity

only_image - Input: if true, only the image term is considered and not the regularization

bIsReverse - Input: flag to determine the transformation direction (target-source=FALSE or source-target=TRUE)

Returns:

images similarity value

evaluateConsistencyMultiThread

private double evaluateConsistencyMultiThread(int intervals,
                                              double[] grad)

Calculate the geometric error between the source-target and target-source deformations. The corresponding coefficients are assumed to be at swxTargetToSource, swyTargetToSource, swxSourceToTarget and swySourceToTarget. Multi-thread version.

Parameters:

intervals - Input: Number of intervals for the deformation

grad - Output: Gradient of the function

Returns:

geometric error between the source-target and target-source deformations.