Transformation (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bunwarpj.Transformation

```
public class Transformation
extends 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 doBidirectionalRegistration (bidirectional) and doUnidirectionalRegistration (unidirectional).
- The intermediate states of the registration are displayed in separate windows (depending on the value of outputLevel.

Constructor Summary

Constructors
Constructor and Description
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, String fn_tnf_1, 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, String fn_tnf_1, 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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`doBidirectionalRegistration()` Registration method.
`void`	`doUnidirectionalRegistration()` Unidirectional registration method.
`double`	`evaluateImageSimilarity(boolean bIsReverse)` Evaluate the similarity between the images.
`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
`void`	`loadDirectTransformation(String fileName)` Load target to source transformation from a file.
`void`	`loadInverseTransformation(String fileName)` Load source to target transformation from a file.
`static AffineTransform`	`makeAffineMatrix(double scalex, double scaley, double shearx, double sheary, double rotang, double transx, double transy)` Makes an affine transformation matrix from the given scale, shear, rotation and translation values if you want a uniquely retrievable matrix, give sheary=0
`void`	`regularizeMatrix(AffineTransform a, double centerX, double centerY)` Regularize matrix to remove sharing, scaling, etc.
`void`	`saveDirectTransformation()` Save source transformation.
`void`	`saveDirectTransformation(String fileName)` Save target to source transformation into a file.
`void`	`saveInverseTransformation()` Save target transformation.
`void`	`saveInverseTransformation(String fileName)` Save source to target transformation into a file.
`void`	`setAnisotropyCorrection(double isoCorrection)` Correct anisotropy on initial affine transform
`void`	`setScaleCorrection(double scaleCorrection)` Correct scale on initial affine transform
`void`	`setShearCorrection(double shearCorrection)` Correct shear on initial affine transform
`void`	`showDirectResults()` Show the direct transformation results(multi-thread version).
`void`	`showInverseResults()` Show the inverse transformation results (multi-thread version).
`void`	`transform(double u, double v, double[] xyF, boolean bIsReverse)` Apply the current transformation to a given point.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- 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,
                      String fn_tnf_1,
                      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,
                      String fn_tnf_1,
                      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
  - doBidirectionalRegistration
```
public void doBidirectionalRegistration()
```
    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. Point coordinates must be in real space (highest resolution). The transformation will take the subsampling factor into account.
    
    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)
  - regularizeMatrix
```
public void regularizeMatrix(AffineTransform a,
                             double centerX,
                             double centerY)
```
    Regularize matrix to remove sharing, scaling, etc.
    
    Parameters:
    
    a - affine transform
    
    centerX - image center x- coordinate
    
    centerX - image center y- coordinate
  - makeAffineMatrix
```
public static AffineTransform makeAffineMatrix(double scalex,
                                               double scaley,
                                               double shearx,
                                               double sheary,
                                               double rotang,
                                               double transx,
                                               double transy)
```
    Makes an affine transformation matrix from the given scale, shear, rotation and translation values if you want a uniquely retrievable matrix, give sheary=0
    
    Parameters:
    
    scalex - scaling in x
    
    scaley - scaling in y
    
    shearx - shearing in x
    
    sheary - shearing in y
    
    rotang - angle of rotation (in radians)
    
    transx - translation in x
    
    transy - translation in y
    
    Returns:
    
    affine transformation matrix
  - saveDirectTransformation
```
public void saveDirectTransformation()
```
    Save source transformation. GUI mode.
  - saveDirectTransformation
```
public void saveDirectTransformation(String fileName)
```
    Save target to source transformation into a file.
  - saveInverseTransformation
```
public void saveInverseTransformation()
```
    Save target transformation. GUI mode.
  - saveInverseTransformation
```
public void saveInverseTransformation(String fileName)
```
    Save source to target transformation into a file.
  - loadDirectTransformation
```
public void loadDirectTransformation(String fileName)
```
    Load target to source transformation from a file.
  - loadInverseTransformation
```
public void loadInverseTransformation(String fileName)
```
    Load source to target transformation from a file.
  - showDirectResults
```
public void showDirectResults()
```
    Show the direct transformation results(multi-thread version).
  - showInverseResults
```
public void showInverseResults()
```
    Show the inverse transformation results (multi-thread version).
  - 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
  - setShearCorrection
```
public void setShearCorrection(double shearCorrection)
```
    Correct shear on initial affine transform
    
    Parameters:
    
    shearCorrection - percentage of shear correction (0.0 - 1.0)
  - setScaleCorrection
```
public void setScaleCorrection(double scaleCorrection)
```
    Correct scale on initial affine transform
    
    Parameters:
    
    scaleCorrection - percentage of scale correction (0.0 - 1.0)
  - setAnisotropyCorrection
```
public void setAnisotropyCorrection(double isoCorrection)
```
    Correct anisotropy on initial affine transform
    
    Parameters:
    
    isoCorrection - percentage of anisotropy correction (0.0 - 1.0)

Class Transformation

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Transformation

Transformation

Method Detail

doBidirectionalRegistration

doUnidirectionalRegistration

evaluateImageSimilarity

getDeformation

getDirectDeformationCoefficientsX

getDirectDeformationCoefficientsY

getInverseDeformationCoefficientsX

getInverseDeformationCoefficientsY

getIntervals

transform

regularizeMatrix

makeAffineMatrix

saveDirectTransformation

saveDirectTransformation

saveInverseTransformation

saveInverseTransformation

loadDirectTransformation

loadInverseTransformation

showDirectResults

showInverseResults

getDirectResults

getInverseResults

setShearCorrection

setScaleCorrection

setAnisotropyCorrection