bunwarpj
Class MiscTools

java.lang.Object
  bunwarpj.MiscTools

public class MiscTools
extends java.lang.Object

Different tools for the bUnwarpJ interface.

Nested Class Summary

private static class	MiscTools.ColorApplyTransformTile Class to apply transformation to color images in a concurrent way
private static class	MiscTools.GrayscaleApplyTransformTile Class to apply transformation to grayscale images in a concurrent way

Constructor Summary

MiscTools()

Method Summary

static void	adaptCoefficients(double xScale, double yScale, int intervals, double[][] cx, double[][] cy) Adapt B-spline coefficients to a scale factor
static void	applyRawTransformationToSource(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, BSplineModel source, double[][] transformation_x, double[][] transformation_y) Apply a given raw transformation to the source image.
static ij.process.ImageProcessor	applyTransformationMT(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, BSplineModel source, int intervals, double[][] cx, double[][] cy) Apply a given B-spline transformation to the source (gray-scale) image.
static void	applyTransformationToSource(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, BSplineModel sourceR, BSplineModel sourceG, BSplineModel sourceB, int intervals, double[][] cx, double[][] cy) Deprecated.
static void	applyTransformationToSource(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, BSplineModel source, int intervals, double[][] cx, double[][] cy) Deprecated.
static void	applyTransformationToSourceMT(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, BSplineModel source, int intervals, double[][] cx, double[][] cy) Apply a given B-spline transformation to the source (gray-scale) image.
static void	applyTransformationToSourceMT(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, int intervals, double[][] cx, double[][] cy) Apply a given B-spline transformation to the source (gray-scale) image.
static void	composeElasticTransformations(ij.ImagePlus targetImp, int intervals, double[][] cx1, double[][] cy1, double[][] cx2, double[][] cy2, double[][] outputTransformation_x, double[][] outputTransformation_y) Compose two elastic deformations into a raw deformation.
static void	composeElasticTransformationsAtPixelLevel(ij.ImagePlus targetImp, int intervals, double[][] cx1, double[][] cy1, double[][] cx2, double[][] cy2, double[][] outputTransformation_x, double[][] outputTransformation_y) Compose two elastic deformations into a raw deformation at pixel level.
static void	composeRawElasticTransformations(ij.ImagePlus targetImp, int intervals, double[][] transformation_x_1, double[][] transformation_y_1, double[][] cx2, double[][] cy2, double[][] outputTransformation_x, double[][] outputTransformation_y) Compose a raw deformation and an elastic deformation into a raw deformation.
static void	composeRawTransformations(int width, int height, double[][] transformation_x_1, double[][] transformation_y_1, double[][] transformation_x_2, double[][] transformation_y_2, double[][] outputTransformation_x, double[][] outputTransformation_y) Compose two raw transformations (Bilinear interpolation)
static void	convertElasticTransformationToRaw(ij.ImagePlus targetImp, int intervals, double[][] cx, double[][] cy, double[][] transformation_x, double[][] transformation_y) Calculate the raw transformation mapping from B-spline coefficients.
static void	convertRawTransformationToBSpline(ij.ImagePlus targetImp, int intervals, double[][] transformation_x, double[][] transformation_y, double[][] cx, double[][] cy) Convert the raw transformation mapping to B-spline coefficients.
static ij.process.ImageProcessor	createDownsampled(ij.process.ImageProcessor source, float scale, float sourceSigma, float targetSigma) Create a downsampled ImageProcessor.
static void	drawArrow(double[][] canvas, int x1, int y1, int x2, int y2, double color, int arrow_size) Draw an arrow between two points.
static void	drawLine(double[][] canvas, int x1, int y1, int x2, int y2, double color) Draw a line between two points.
static void	extractImage(ij.process.ImageProcessor ip, double[] image) Put the image from an ImageProcessor into a double array.
static void	extractImage(ij.process.ImageProcessor ip, double[][] image) Put the image from an ImageProcessor into a double[][].
static void	invertRawTransformation(ij.ImagePlus targetImp, double[][] transformation_x, double[][] transformation_y, double[][] inv_x, double[][] inv_y)
static void	loadAffineMatrix(java.lang.String filename, double[][] affineMatrix) Load an affine matrix from a file.
static void	loadPointRoiAsLandmarks(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, java.util.Stack<java.awt.Point> sourceStack, java.util.Stack<java.awt.Point> targetStack) Load point rois in the source and target images as landmarks.
static void	loadPoints(java.lang.String filename, java.util.Stack<java.awt.Point> sourceStack, java.util.Stack<java.awt.Point> targetStack) Load landmarks from file.
static void	loadRawTransformation(java.lang.String filename, double[][] transformation_x, double[][] transformation_y) Load a raw transformation from a file.
static void	loadRawTransformation(java.lang.String filename, double[] transformation_x, double[] transformation_y) Load a raw transformation from a file.
static void	loadTransformation(java.lang.String filename, double[][] cx, double[][] cy) Load a transformation from a file.
static int	numberOfIntervalsOfTransformation(java.lang.String filename) Read the number of intervals of a transformation from a file.
static void	Point(double[][] canvas, int y, int x, double color) Plot a point in a canvas.
static void	printMatrix(java.lang.String title, double[][] array) Print a matrix in the command line.
static double	rawWarpingIndex(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, double[][] transformation_x_1, double[][] transformation_y_1, double[][] transformation_x_2, double[][] transformation_y_2) Warping index for comparing two raw deformations (both transformations having same direction).
static double	rawWarpingIndex(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, int intervals, double[][] cx_direct, double[][] cy_direct, double[][] transformation_x, double[][] transformation_y) Warping index for comparing elastic deformations with any kind of deformation (both transformations having same direction).
static void	saveElasticTransformation(int intervals, double[][] cx, double[][] cy, java.lang.String filename) Save the elastic transformation.
static void	saveRawTransformation(java.lang.String filename, int width, int height, double[][] transformation_x, double[][] transformation_y) Save a raw transformation
static ij.process.ImageProcessor	scale(ij.process.ImageProcessor source, float scale) Scale an image with good quality in both up and down direction
static void	showImage(java.lang.String title, double[][] array) Show an image in a new bUnwarpJ window.
static void	showImage(java.lang.String title, double[] array, int Ydim, int Xdim) Show an image in a new bUnwarpJ window.
static void	smoothForScale(ij.process.ImageProcessor source, float scale, float sourceSigma, float targetSigma) Smooth with a Gaussian kernel that represents downsampling at a given scale factor and sourceSigma.
static double	warpingIndex(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, int intervals, double[][] cx_direct, double[][] cy_direct, double[][] cx_inverse, double[][] cy_inverse) Calculate the warping index between two opposite elastic deformations.

Methods inherited from class java.lang.Object

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

Constructor Detail

MiscTools

public MiscTools()

Method Detail

applyTransformationToSource

public static void applyTransformationToSource(ij.ImagePlus sourceImp,
                                               ij.ImagePlus targetImp,
                                               BSplineModel source,
                                               int intervals,
                                               double[][] cx,
                                               double[][] cy)

Deprecated.

Apply a given B-spline transformation to the source (gray-scale) image. The source image is modified. The target image is used to know the output size.

Parameters:

sourceImp - source image representation

targetImp - target image representation

source - source image model

intervals - intervals in the deformation

cx - x- B-spline coefficients

cy - y- B-spline coefficients

applyTransformationToSource

public static void applyTransformationToSource(ij.ImagePlus sourceImp,
                                               ij.ImagePlus targetImp,
                                               BSplineModel sourceR,
                                               BSplineModel sourceG,
                                               BSplineModel sourceB,
                                               int intervals,
                                               double[][] cx,
                                               double[][] cy)

Deprecated.

Apply a given splines transformation to the source (RGB color) image. The source image is modified. The target image is used to know the output size.

Parameters:

sourceImp - source image representation

targetImp - target image representation

sourceR - image model of the source red channel

sourceG - image model of the source green channel

sourceB - image model of the source blue channel

intervals - intervals in the deformation

cx - x- B-spline coefficients

cy - y- B-spline coefficients

applyRawTransformationToSource

public static void applyRawTransformationToSource(ij.ImagePlus sourceImp,
                                                  ij.ImagePlus targetImp,
                                                  BSplineModel source,
                                                  double[][] transformation_x,
                                                  double[][] transformation_y)

Apply a given raw transformation to the source image. The source image is modified. The target image is used to know the output size.

Parameters:

sourceImp - source image representation

targetImp - target image representation

source - source image

transformation_x - x- mapping coordinates

transformation_y - y- mapping coordinates

warpingIndex

public static double warpingIndex(ij.ImagePlus sourceImp,
                                  ij.ImagePlus targetImp,
                                  int intervals,
                                  double[][] cx_direct,
                                  double[][] cy_direct,
                                  double[][] cx_inverse,
                                  double[][] cy_inverse)

Calculate the warping index between two opposite elastic deformations. Note: the only difference between the warping index and the consistency term formulae is a squared root: warping index = sqrt(consistency error).

Parameters:

sourceImp - source image representation

targetImp - target image representation

intervals - intervals in the deformation

cx_direct - direct transformation x- B-spline coefficients

cy_direct - direct transformation y- B-spline coefficients

cx_inverse - inverse transformation x- B-spline coefficients

cy_inverse - inverse transformation y- B-spline coefficients

Returns:

geometric error (warping index) between both deformations.

convertElasticTransformationToRaw

public static void convertElasticTransformationToRaw(ij.ImagePlus targetImp,
                                                     int intervals,
                                                     double[][] cx,
                                                     double[][] cy,
                                                     double[][] transformation_x,
                                                     double[][] transformation_y)

Calculate the raw transformation mapping from B-spline coefficients.

Parameters:

targetImp - target image representation

intervals - intervals in the deformation

cx - transformation x- B-spline coefficients

cy - transformation y- B-spline coefficients

transformation_x - raw transformation in x- axis (output)

transformation_y - raw transformation in y- axis (output)

convertRawTransformationToBSpline

public static void convertRawTransformationToBSpline(ij.ImagePlus targetImp,
                                                     int intervals,
                                                     double[][] transformation_x,
                                                     double[][] transformation_y,
                                                     double[][] cx,
                                                     double[][] cy)

Convert the raw transformation mapping to B-spline coefficients.

Parameters:

targetImp - target image representation

intervals - intervals in the deformation

transformation_x - raw transformation in x- axis

transformation_y - raw transformation in y- axis

cx - transformation in x- by B-spline coefficients (output)

cy - transformation in y- by B-spline coefficients (output)

invertRawTransformation

public static void invertRawTransformation(ij.ImagePlus targetImp,
                                           double[][] transformation_x,
                                           double[][] transformation_y,
                                           double[][] inv_x,
                                           double[][] inv_y)

rawWarpingIndex

public static double rawWarpingIndex(ij.ImagePlus sourceImp,
                                     ij.ImagePlus targetImp,
                                     int intervals,
                                     double[][] cx_direct,
                                     double[][] cy_direct,
                                     double[][] transformation_x,
                                     double[][] transformation_y)

Warping index for comparing elastic deformations with any kind of deformation (both transformations having same direction).

Parameters:

sourceImp - source image representation

targetImp - target image representation

intervals - intervals in the deformation

cx_direct - direct transformation x- B-spline coefficients

cy_direct - direct transformation y- B-spline coefficients

transformation_x - raw direct transformation in x- axis

transformation_y - raw direct transformation in y- axis

rawWarpingIndex

public static double rawWarpingIndex(ij.ImagePlus sourceImp,
                                     ij.ImagePlus targetImp,
                                     double[][] transformation_x_1,
                                     double[][] transformation_y_1,
                                     double[][] transformation_x_2,
                                     double[][] transformation_y_2)

Warping index for comparing two raw deformations (both transformations having same direction).

Parameters:

sourceImp - source image representation

targetImp - target image representation

transformation_x_1 - raw first transformation in x- axis

transformation_y_1 - raw first transformation in y- axis

transformation_x_2 - raw second transformation in x- axis

transformation_y_2 - raw second transformation in y- axis

drawArrow

public static void drawArrow(double[][] canvas,
                             int x1,
                             int y1,
                             int x2,
                             int y2,
                             double color,
                             int arrow_size)

Draw an arrow between two points. The arrow head is in (x2,y2)

Parameters:

canvas - canvas where we are painting

x1 - x- coordinate for the arrow origin

y1 - y- coordinate for the arrow origin

x2 - x- coordinate for the arrow head

y2 - y- coordinate for the arrow head

color - arrow color

arrow_size - arrow size

drawLine

public static void drawLine(double[][] canvas,
                            int x1,
                            int y1,
                            int x2,
                            int y2,
                            double color)

Draw a line between two points. Bresenham's algorithm.

Parameters:

canvas - canvas where we are painting

x1 - x- coordinate for first point

y1 - y- coordinate for first point

x2 - x- coordinate for second point

y2 - y- coordinate for second point

color - line color

extractImage

public static void extractImage(ij.process.ImageProcessor ip,
                                double[] image)

Put the image from an ImageProcessor into a double array.

Parameters:

ip - input, origin of the image

image - output, the image in a double array

extractImage

public static void extractImage(ij.process.ImageProcessor ip,
                                double[][] image)

Put the image from an ImageProcessor into a double[][].

Parameters:

ip - input, origin of the image

image - output, the image in a double[][]

loadPoints

public static void loadPoints(java.lang.String filename,
                              java.util.Stack<java.awt.Point> sourceStack,
                              java.util.Stack<java.awt.Point> targetStack)

Load landmarks from file.

Parameters:

filename - landmarks file name

sourceStack - stack of source related points (output)

targetStack - stack of target related points (output)

loadPointRoiAsLandmarks

public static void loadPointRoiAsLandmarks(ij.ImagePlus sourceImp,
                                           ij.ImagePlus targetImp,
                                           java.util.Stack<java.awt.Point> sourceStack,
                                           java.util.Stack<java.awt.Point> targetStack)

Load point rois in the source and target images as landmarks.

Parameters:

sourceImp - source image plus

targetImp - target image plus

sourceStack - stack of source related points (output)

targetStack - stack of target related points (output)

loadTransformation

public static void loadTransformation(java.lang.String filename,
                                      double[][] cx,
                                      double[][] cy)

Load a transformation from a file.

Parameters:

filename - transformation file name

cx - x- B-spline coefficients

cy - y- B-spline coefficients

loadRawTransformation

public static void loadRawTransformation(java.lang.String filename,
                                         double[][] transformation_x,
                                         double[][] transformation_y)

Load a raw transformation from a file.

Parameters:

filename - transformation file name

transformation_x - output x- transformation coordinates

transformation_y - output y- transformation coordinates

loadRawTransformation

public static void loadRawTransformation(java.lang.String filename,
                                         double[] transformation_x,
                                         double[] transformation_y)

Load a raw transformation from a file.

Parameters:

filename - transformation file name

transformation_x - output x- transformation coordinates

transformation_y - output y- transformation coordinates

loadAffineMatrix

public static void loadAffineMatrix(java.lang.String filename,
                                    double[][] affineMatrix)

Load an affine matrix from a file.

Parameters:

filename - matrix file name

affineMatrix - output affine matrix

composeElasticTransformations

public static void composeElasticTransformations(ij.ImagePlus targetImp,
                                                 int intervals,
                                                 double[][] cx1,
                                                 double[][] cy1,
                                                 double[][] cx2,
                                                 double[][] cy2,
                                                 double[][] outputTransformation_x,
                                                 double[][] outputTransformation_y)

Compose two elastic deformations into a raw deformation.

Parameters:

targetImp - target image representation

intervals - intervals in the deformation

cx1 - first transformation x- B-spline coefficients

cy1 - first transformation y- B-spline coefficients

cx2 - second transformation x- B-spline coefficients

cy2 - second transformation y- B-spline coefficients

outputTransformation_x - output transformation coordinates in x-axis

outputTransformation_y - output transformation coordinates in y-axis

composeRawElasticTransformations

public static void composeRawElasticTransformations(ij.ImagePlus targetImp,
                                                    int intervals,
                                                    double[][] transformation_x_1,
                                                    double[][] transformation_y_1,
                                                    double[][] cx2,
                                                    double[][] cy2,
                                                    double[][] outputTransformation_x,
                                                    double[][] outputTransformation_y)

Compose a raw deformation and an elastic deformation into a raw deformation.

Parameters:

targetImp - target image representation

intervals - intervals in the deformation

transformation_x_1 - first transformation coordinates in x-axis

transformation_y_1 - first transformation coordinates in y-axis

cx2 - second transformation x- B-spline coefficients

cy2 - second transformation y- B-spline coefficients

outputTransformation_x - output transformation coordinates in x-axis

outputTransformation_y - output transformation coordinates in y-axis

composeElasticTransformationsAtPixelLevel

public static void composeElasticTransformationsAtPixelLevel(ij.ImagePlus targetImp,
                                                             int intervals,
                                                             double[][] cx1,
                                                             double[][] cy1,
                                                             double[][] cx2,
                                                             double[][] cy2,
                                                             double[][] outputTransformation_x,
                                                             double[][] outputTransformation_y)

Compose two elastic deformations into a raw deformation at pixel level.

Parameters:

targetImp - target image representation

intervals - intervals in the deformation

cx1 - first transformation x- B-spline coefficients

cy1 - first transformation y- B-spline coefficients

cx2 - second transformation x- B-spline coefficients

cy2 - second transformation y- B-spline coefficients

outputTransformation_x - output transformation coordinates in y-axis

outputTransformation_y - output transformation coordinates in y-axis

composeRawTransformations

public static void composeRawTransformations(int width,
                                             int height,
                                             double[][] transformation_x_1,
                                             double[][] transformation_y_1,
                                             double[][] transformation_x_2,
                                             double[][] transformation_y_2,
                                             double[][] outputTransformation_x,
                                             double[][] outputTransformation_y)

Compose two raw transformations (Bilinear interpolation)

Parameters:

width - image width

height - image height

transformation_x_1 - first transformation coordinates in x-axis

transformation_y_1 - first transformation coordinates in y-axis

transformation_x_2 - second transformation coordinates in x-axis

transformation_y_2 - second transformation coordinates in y-axis

outputTransformation_x - output transformation coordinates in y-axis

outputTransformation_y - output transformation coordinates in y-axis

saveElasticTransformation

public static void saveElasticTransformation(int intervals,
                                             double[][] cx,
                                             double[][] cy,
                                             java.lang.String filename)

Save the elastic transformation.

Parameters:

intervals - number of intervals in the deformation

cx - x- deformation coefficients

cy - y- deformation coefficients

filename - transformation file name

saveRawTransformation

public static void saveRawTransformation(java.lang.String filename,
                                         int width,
                                         int height,
                                         double[][] transformation_x,
                                         double[][] transformation_y)

Save a raw transformation

Parameters:

filename - raw transformation file name

width - image width

height - image height

transformation_x - transformation coordinates in x-axis

transformation_y - transformation coordinates in y-axis

numberOfIntervalsOfTransformation

public static int numberOfIntervalsOfTransformation(java.lang.String filename)

Read the number of intervals of a transformation from a file.

Parameters:

filename - transformation file name

Returns:

number of intervals

Point

public static void Point(double[][] canvas,
                         int y,
                         int x,
                         double color)

Plot a point in a canvas.

Parameters:

canvas - canvas where we are painting

x - x- coordinate for the point

y - y- coordinate for the point

color - point color

printMatrix

public static void printMatrix(java.lang.String title,
                               double[][] array)

Print a matrix in the command line.

Parameters:

title - matrix title

array - matrix to be printed

showImage

public static void showImage(java.lang.String title,
                             double[] array,
                             int Ydim,
                             int Xdim)

Show an image in a new bUnwarpJ window.

Parameters:

title - image title

array - image in a double array

Ydim - image height

Xdim - image width

showImage

public static void showImage(java.lang.String title,
                             double[][] array)

Show an image in a new bUnwarpJ window.

Parameters:

title - image title

array - image in a double array

adaptCoefficients

public static void adaptCoefficients(double xScale,
                                     double yScale,
                                     int intervals,
                                     double[][] cx,
                                     double[][] cy)

Adapt B-spline coefficients to a scale factor

Parameters:

xScale -

yScale -

intervals -

cx -

cy -

applyTransformationToSourceMT

public static void applyTransformationToSourceMT(ij.ImagePlus sourceImp,
                                                 ij.ImagePlus targetImp,
                                                 int intervals,
                                                 double[][] cx,
                                                 double[][] cy)

Apply a given B-spline transformation to the source (gray-scale) image. The source image is modified. The target image is used to know the output size (Multi-thread version).

Parameters:

sourceImp - source image representation

targetImp - target image representation

intervals - intervals in the deformation

cx - x- B-spline coefficients

cy - y- B-spline coefficients

applyTransformationToSourceMT

public static void applyTransformationToSourceMT(ij.ImagePlus sourceImp,
                                                 ij.ImagePlus targetImp,
                                                 BSplineModel source,
                                                 int intervals,
                                                 double[][] cx,
                                                 double[][] cy)

Apply a given B-spline transformation to the source (gray-scale) image. The source image is modified. The target image is used to know the output size (Multi-thread version).

Parameters:

sourceImp - source image representation

targetImp - target image representation

source - source image model

intervals - intervals in the deformation

cx - x- B-spline coefficients

cy - y- B-spline coefficients

applyTransformationMT

public static ij.process.ImageProcessor applyTransformationMT(ij.ImagePlus sourceImp,
                                                              ij.ImagePlus targetImp,
                                                              BSplineModel source,
                                                              int intervals,
                                                              double[][] cx,
                                                              double[][] cy)

Apply a given B-spline transformation to the source (gray-scale) image. The result image is return. The target image is used to know the output size (Multi-thread version).

Parameters:

sourceImp - source image representation

targetImp - target image representation

source - source image model

intervals - intervals in the deformation

cx - x- B-spline coefficients

cy - y- B-spline coefficients

Returns:

result transformed image

smoothForScale

public static final void smoothForScale(ij.process.ImageProcessor source,
                                        float scale,
                                        float sourceSigma,
                                        float targetSigma)

Smooth with a Gaussian kernel that represents downsampling at a given scale factor and sourceSigma.

createDownsampled

public static final ij.process.ImageProcessor createDownsampled(ij.process.ImageProcessor source,
                                                                float scale,
                                                                float sourceSigma,
                                                                float targetSigma)

Create a downsampled ImageProcessor.

Parameters:

source - the source image

scale - scaling factor

sourceSigma - the Gaussian at which the source was sampled (guess 0.5 if you do not know)

targetSigma - the Gaussian at which the target will be sampled

Returns:

a new FloatProcessor

scale

public static final ij.process.ImageProcessor scale(ij.process.ImageProcessor source,
                                                    float scale)

Scale an image with good quality in both up and down direction