MiscTools (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bunwarpj.MiscTools

```
public class MiscTools
extends Object
```
Different tools for the bUnwarpJ interface.

Constructor Summary

Constructors
Constructor and Description

MiscTools()

Constructors
Constructor and Description
`MiscTools()`

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`static void`	`adaptCoefficients(double xScale, double yScale, int intervals, double[][] cx, double[][] cy)` Adapt B-spline coefficients to a scale factor
`static void`	`adaptCoefficients(String inputTransfPath, double scaleFactor, String outputTransfPath)` Adapt B-spline coefficients based on 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 ij.ImagePlus`	`applyTransformToStack(String transformationFile, ij.ImagePlus fixedImage, ij.ImagePlus movingStack)` Apply transform saved on a file to all slices of moving image
`static double[]`	`approximateInverseCoords(double[] movingCoords, ij.ImagePlus fixedImp, double[][] transformation_x, double[][] transformation_y)` Approximate the transformed coordinates of a point from the moving image into the fixed 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`	`composeElasticTransforms(String elasticTransfPath1, String elasticTransfPath2, String outputRawTransfPath, ij.ImagePlus targetImp)` Compose two elastic transform into a raw transform and save it to file
`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`	`composeRawElasticTransforms(String rawTransfPath, String elasticTransfPath, String outputPath, ij.ImagePlus targetImp, ij.ImagePlus sourceImp)` Compose a raw and an elastic transform and save result into file.
`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`	`composeRawTransforms(String transfPath1, String transfPath2, String outputTransfPath, ij.ImagePlus targetImp)` Compose raw transforms into another raw transform and save to file.
`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 double`	`elasticRawWarpingIndex(String elasticTransfPath, String rawTransfPath, ij.ImagePlus targetImp, ij.ImagePlus sourceImp)` Calculate warping index between an elastic and a raw transform loaded from file.
`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 String`	`getUserSelectedFilePath(String dialogTitle, boolean saveDialog)` Show a non-recordable dialog so the user selects a file.
`static double`	`imageSimilarity(ij.ImagePlus targetImp, ij.ImagePlus sourceImp, Mask targetMsk, boolean verbose)` Calculate image similarity between two images (target and source)
`static void`	`invertRawTransformation(ij.ImagePlus targetImp, double[][] transformation_x, double[][] transformation_y, double[][] inv_x, double[][] inv_y)`
`static void`	`invertRawTransformation(String inputTransfPath, String outputTransfPath, ij.ImagePlus targetImp)` Approximate the inverse of a raw transform and save it to file.
`static void`	`loadAffineMatrix(String filename, double[][] affineMatrix)` Load an affine matrix from a file.
`static void`	`loadPointRoiAsLandmarks(ij.ImagePlus sourceImp, ij.ImagePlus targetImp, Stack<Point> sourceStack, Stack<Point> targetStack)` Load point rois in the source and target images as landmarks.
`static void`	`loadPoints(String filename, Stack<Point> sourceStack, Stack<Point> targetStack)` Load landmarks from file.
`static void`	`loadRawTransformation(String filename, double[][] transformation_x, double[][] transformation_y)` Load a raw transformation from a file.
`static void`	`loadRawTransformation(String filename, double[] transformation_x, double[] transformation_y)` Load a raw transformation from a file.
`static void`	`loadTransformation(String filename, double[][] cx, double[][] cy)` Load a transformation from a file.
`static int`	`numberOfIntervalsOfTransformation(String filename)` Read the number of intervals of a transformation from a file.
`static double`	`oppositeWarpingIndex(String directTransfPath, String inverseTransfPath, ij.ImagePlus targetImp, ij.ImagePlus sourceImp)` Calculate the warping index between two opposite elastic deformations.
`static void`	`Point(double[][] canvas, int y, int x, double color)` Plot a point in a canvas.
`static void`	`printMatrix(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 double`	`rawWarpingIndex(String rawTransfPath1, String rawTransfPath2, ij.ImagePlus targetImp, ij.ImagePlus sourceImp)` Calculate warping index between two raw transforms loaded from file.
`static void`	`saveElasticAsRaw(String elasticTransfPath, String rawTransfPath, ij.ImagePlus targetImp)` Save elastic transform as raw transform.
`static void`	`saveElasticTransformation(int intervals, double[][] cx, double[][] cy, String filename)` Save the elastic transformation.
`static void`	`saveLandmarks(String outputPath, Vector<Point> sourceList, Vector<Point> targetList)` Save source and target landmarks to file
`static void`	`saveRawAsElastic(String rawTransfPath, String elasticTransfPath, int intervals, ij.ImagePlus targetImp)` Save raw transform as elastic.
`static void`	`saveRawTransformation(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(String title, double[][] array)` Show an image in a new bUnwarpJ window.
`static void`	`showImage(String title, double[] array, int Ydim, int Xdim)` Show an image in a new bUnwarpJ window.
`static void`	`showPoints(Vector<Point> sourceList, Vector<Point> targetList)` Display landmark points in a separate table
`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

approximateInverseCoords
```
public static double[] approximateInverseCoords(double[] movingCoords,
                                                ij.ImagePlus fixedImp,
                                                double[][] transformation_x,
                                                double[][] transformation_y)
```
Approximate the transformed coordinates of a point from the moving image into the fixed image. Notice the raw transform stores for each fixed image position the coordinates of the corresponding moving pixel to fill it in. Therefore the new position of the moving (source) point in fixed (target) space can be approximated by finding the closest point in the transform.

Parameters:

movingCoords - point coordinates in moving space

fixedImp - fixed (source) image

transformation_x - raw transform x-coordinates

transformation_y - raw transform y-coordinates

Returns:

approximated position of the point after transformation

oppositeWarpingIndex
```
public static double oppositeWarpingIndex(String directTransfPath,
                                          String inverseTransfPath,
                                          ij.ImagePlus targetImp,
                                          ij.ImagePlus sourceImp)
```
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:

directTransfPath - complete path to direct elastic transform

inverseTransfPath - complete path to inverse elastic transform

targetImp - target image

sourceImp - source image

Returns:

geometric error (warping index) between both deformations

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.

saveElasticAsRaw

public static void saveElasticAsRaw(String elasticTransfPath,
                                    String rawTransfPath,
                                    ij.ImagePlus targetImp)

Save elastic transform as raw transform.

Parameters:: elasticTransfPath - complete path to elastic transform; rawTransfPath - complete path to raw transform; targetImp - target image

saveRawAsElastic

public static void saveRawAsElastic(String rawTransfPath,
                                    String elasticTransfPath,
                                    int intervals,
                                    ij.ImagePlus targetImp)

Save raw transform as elastic.

Parameters:: rawTransfPath - complete path to input raw transform; elasticTransfPath - complete path to output elastic transform; intervals - number of intervals between B-spline coefficients; targetImp - target image

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)

invertRawTransformation

public static void invertRawTransformation(String inputTransfPath,
                                           String outputTransfPath,
                                           ij.ImagePlus targetImp)

Approximate the inverse of a raw transform and save it to file.

Parameters:: inputTransfPath - complete path to input raw transform file; outputTransfPath - complete path to output transform file; targetImp - target image

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(String filename,
                              Stack<Point> sourceStack,
                              Stack<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,
                                           Stack<Point> sourceStack,
                                           Stack<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(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(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(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(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

composeRawTransforms

public static void composeRawTransforms(String transfPath1,
                                        String transfPath2,
                                        String outputTransfPath,
                                        ij.ImagePlus targetImp)

Compose raw transforms into another raw transform and save to file.

Parameters:: transfPath1 - complete path to first raw transform; transfPath2 - complete path to second raw transform; outputTransfPath - complete path to output file; targetImp - target image

composeElasticTransforms

public static void composeElasticTransforms(String elasticTransfPath1,
                                            String elasticTransfPath2,
                                            String outputRawTransfPath,
                                            ij.ImagePlus targetImp)

Compose two elastic transform into a raw transform and save it to file

Parameters:: elasticTransfPath1 - complete path to first elastic transform; elasticTransfPath2 - complete path to second elastic transform; outputRawTransfPath - complete path to output raw transform file; targetImp - target image

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,
                                             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(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(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(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(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(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(String inputTransfPath,
                                     double scaleFactor,
                                     String outputTransfPath)

Adapt B-spline coefficients based on a scale factor.

Parameters:: inputTransfPath - complete path to input transform file; scaleFactor - isotropic scale factor; outputTransfPath - complete path to output transform file

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

applyTransformToStack
```
public static ij.ImagePlus applyTransformToStack(String transformationFile,
                                                 ij.ImagePlus fixedImage,
                                                 ij.ImagePlus movingStack)
```
Apply transform saved on a file to all slices of moving image

Parameters:

transformationFile - elastic transform file

fixedImage - fixed image

movingStack - stack containing all the moving images

Returns:

stack containing the deformed slices

imageSimilarity

public static double imageSimilarity(ij.ImagePlus targetImp,
                                     ij.ImagePlus sourceImp,
                                     Mask targetMsk,
                                     boolean verbose)

Calculate image similarity between two images (target and source)

Parameters:: targetImp - target image; sourceImp - source image; targetMsk - target mask; verbose - flag to display result in log window
Returns:: image similarity value or -1 if error

saveLandmarks

public static void saveLandmarks(String outputPath,
                                 Vector<Point> sourceList,
                                 Vector<Point> targetList)

Save source and target landmarks to file

Parameters:: outputPath - complete output landmark path; sourceList - vector of source landmark points; targetList - vector of target landmark points

showPoints
```
public static void showPoints(Vector<Point> sourceList,
                              Vector<Point> targetList)
```
Display landmark points in a separate table

Parameters:

sourceList - vector of source landmark points

targetList - vector of target landmark points

getUserSelectedFilePath
```
public static String getUserSelectedFilePath(String dialogTitle,
                                             boolean saveDialog)
```
Show a non-recordable dialog so the user selects a file.

Parameters:

dialogTitle - displayed dialog title

saveDialog - flag to create save (if true) or load dialog

Returns:

complete path to file or null if dialog is cancelled.

elasticRawWarpingIndex

public static double elasticRawWarpingIndex(String elasticTransfPath,
                                            String rawTransfPath,
                                            ij.ImagePlus targetImp,
                                            ij.ImagePlus sourceImp)

Calculate warping index between an elastic and a raw transform loaded from file.

Parameters:: elasticTransfPath - complete path of elastic transform file; rawTransfPath - complete path of raw transform file; targetImp - target image; sourceImp - source image
Returns:: warping index

rawWarpingIndex
```
public static double rawWarpingIndex(String rawTransfPath1,
                                     String rawTransfPath2,
                                     ij.ImagePlus targetImp,
                                     ij.ImagePlus sourceImp)
```
Calculate warping index between two raw transforms loaded from file. Both transforms have the same direction.

Parameters:

rawTransfPath1 - complete path of first raw transform file

rawTransfPath2 - complete path of second raw transform file

targetImp - target image

sourceImp - source image

Returns:

warping index

composeRawElasticTransforms

public static void composeRawElasticTransforms(String rawTransfPath,
                                               String elasticTransfPath,
                                               String outputPath,
                                               ij.ImagePlus targetImp,
                                               ij.ImagePlus sourceImp)

Compose a raw and an elastic transform and save result into file.

Parameters:: rawTransfPath - complete path to raw transform; elasticTransfPath - complete path to elastic transform; outputPath - complete output file path; targetImp - target image; sourceImp - source image

Class MiscTools

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MiscTools

Method Detail

applyTransformationToSource

applyTransformationToSource

applyRawTransformationToSource

approximateInverseCoords

oppositeWarpingIndex

warpingIndex

saveElasticAsRaw

saveRawAsElastic

convertElasticTransformationToRaw

convertRawTransformationToBSpline

invertRawTransformation

invertRawTransformation

rawWarpingIndex

rawWarpingIndex

drawArrow

drawLine

extractImage

extractImage

loadPoints

loadPointRoiAsLandmarks

loadTransformation

loadRawTransformation

loadRawTransformation

loadAffineMatrix

composeElasticTransformations

composeRawElasticTransformations

composeElasticTransformationsAtPixelLevel

composeRawTransforms

composeElasticTransforms

composeRawTransformations

saveElasticTransformation

saveRawTransformation

numberOfIntervalsOfTransformation

Point

printMatrix

showImage

showImage

adaptCoefficients

adaptCoefficients

applyTransformationToSourceMT

applyTransformationToSourceMT

applyTransformationMT

smoothForScale

createDownsampled

scale

applyTransformToStack

imageSimilarity

saveLandmarks

showPoints

getUserSelectedFilePath

elasticRawWarpingIndex

rawWarpingIndex

composeRawElasticTransforms