bUnwarpJ_ (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bunwarpj.bUnwarpJ_

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class bUnwarpJ_
extends Object
implements ij.plugin.PlugIn
```
Main class for the image registration plugin for ImageJ/Fiji.
This class is a plugin for the ImageJ/Fiji interface. It allows pairwise image registration combining the ideas of elastic registration based on B-spline models and consistent registration.
This work is an extension by Ignacio Arganda-Carreras and Jan Kybic of the previous UnwarpJ project by Carlos Oscar Sanchez Sorzano.
For more information visit the main site http://imagej.net/BUnwarpJ/

Author:

Ignacio Arganda-Carreras

Constructor Summary

Constructors
Constructor and Description

bUnwarpJ_()

Constructors
Constructor and Description
`bUnwarpJ_()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`adaptCoefficients(String inputTransfPath, String strImageFactor, String outputTransfPath)` Adapt the B-spline coefficients to a new image size.
`static void`	`adaptCoefficientsMacro(String targetImageName, String sourceImageName, String inputElasticTransfFileName, String outputElasticTransfFileName, String sizeFactor)` Method to adapt an elastic transformation given a new image size.
`static ij.ImagePlus[]`	`alignImagesBatch(ij.ImagePlus targetImp, ij.ImagePlus sourceImp, ij.process.ImageProcessor targetMskIP, ij.process.ImageProcessor sourceMskIP, int mode, int img_subsamp_fact, int min_scale_deformation, int max_scale_deformation, double divWeight, double curlWeight, double landmarkWeight, double imageWeight, double consistencyWeight, double stopThreshold)` Method for images alignment with no graphical interface.
`static ij.ImagePlus[]`	`alignImagesBatch(ij.ImagePlus targetImp, ij.ImagePlus sourceImp, ij.process.ImageProcessor targetMskIP, ij.process.ImageProcessor sourceMskIP, int mode, int img_subsamp_fact, int min_scale_deformation, int max_scale_deformation, double divWeight, double curlWeight, double landmarkWeight, double imageWeight, double consistencyWeight, double stopThreshold, double xScale, double yScale)` Method for images alignment with no graphical interface.
`static ij.ImagePlus[]`	`alignImagesBatch(ij.ImagePlus targetImp, ij.ImagePlus sourceImp, ij.process.ImageProcessor targetMskIP, ij.process.ImageProcessor sourceMskIP, Param parameter)` Method for images alignment with no graphical interface.
`static void`	`applyRawTransformToSource(String transfPath, ij.ImagePlus targetImp, ij.ImagePlus sourceImp)` Apply a raw transform loaded from file to the source image.
`static void`	`applyTransformToSource(String transfPath, ij.ImagePlus targetImp, ij.ImagePlus sourceImp)` Apply transform loaded from file to source image (in place).
`static void`	`compareElasticRawTransformationsMacro(String targetImageName, String sourceImageName, String targetTransfFileName, String sourceTransfFileName)` Method to compare an elastic and a raw transformations by warping index.
`static void`	`compareElasticRawTransforms(String elasticTransfPath, String rawTransfPath, String targetTitle, String sourceTitle)` Compare an elastic and a raw transform loaded from file.
`static void`	`compareElasticTransformationsMacro(String targetImageName, String sourceImageName, String targetTransfFileName, String sourceTransfFileName)` Method to compare two opposite elastic transformations by warping index.
`static void`	`compareOppositeElasticTransforms(String directTransfPath, String inverseTransfPath, String targetTitle, String sourceTitle)` Compare opposite elastic transforms loaded from file.
`static void`	`compareRawTransformationsMacro(String targetImageName, String sourceImageName, String targetTransfFileName, String sourceTransfFileName)` Method to compare two raw transformations by warping index.
`static void`	`compareRawTransforms(String rawTransfPath1, String rawTransfPath2, String targetTitle, String sourceTitle)` Compare two raw transforms loaded from file.
`static void`	`composeElasticTransformationsMacro(String targetImageName, String sourceImageName, String inputElasticTransfFileName1, String inputElasticTransfFileName2, String outputRawTransfFileName)` Method to compose two elastic transformations.
`static void`	`composeElasticTransforms(String elasticTransfPath1, String elasticTransfPath2, String rawTransfPath, String targetTitle)` Compose two elastic transforms into a raw transform.
`static void`	`composeRawElasticTransformationsMacro(String targetImageName, String sourceImageName, String inputRawTransfFileName, String inputElasticTransfFileName, String outputRawTransfFileName)` Method to compose a raw transformation with an elastic transformation.
`static void`	`composeRawElasticTransforms(String rawTransfPath, String elasticTransfPath, String outputRawTransfPath, String targetTitle, String sourceTitle)` Compose two a raw and an elastic transform into a raw transform.
`static void`	`composeRawTransformationsMacro(String targetImageName, String sourceImageName, String inputRawTransfFileName1, String inputRawTransfFileName2, String outputRawTransfFileName)` Method to compose two raw transformations.
`static void`	`composeRawTransforms(String rawTransfPath1, String rawTransfPath2, String outputRawTransfPath, String targetTitle)` Compose two raw transforms into another raw transform.
`static Transformation`	`computeTransformationBatch(ij.ImagePlus targetImp, ij.ImagePlus sourceImp, ij.process.ImageProcessor targetMskIP, ij.process.ImageProcessor sourceMskIP, AffineTransform targetAffineTransf, AffineTransform sourceAffineTransf, Param parameter)` Method for images alignment with no graphical interface.
`static Transformation`	`computeTransformationBatch(ij.ImagePlus targetImp, ij.ImagePlus sourceImp, ij.process.ImageProcessor targetMskIP, ij.process.ImageProcessor sourceMskIP, int mode, int img_subsamp_fact, int min_scale_deformation, int max_scale_deformation, double divWeight, double curlWeight, double landmarkWeight, double imageWeight, double consistencyWeight, double stopThreshold)` Method for images alignment with no graphical interface.
`static Transformation`	`computeTransformationBatch(ij.ImagePlus targetImp, ij.ImagePlus sourceImp, ij.process.ImageProcessor targetMskIP, ij.process.ImageProcessor sourceMskIP, Param parameter)` Method for images alignment with no graphical interface.
`static Transformation`	`computeTransformationBatch(int sourceWidth, int sourceHeight, int targetWidth, int targetHeight, Stack<Point> sourcePoints, Stack<Point> targetPoints, Param parameter)` Method for images alignment with no graphical interface.
`static void`	`convertToElastic(String rawTransfPath, String elasticTransfPath, String strIntervals, String targetTitle)` Convert an elastic transform to raw format and save it to file.
`static void`	`convertToRaw(String elasticTransfPath, String rawTransfPath, String targetTitle)` Convert an elastic transform to raw format and save it to file.
`static void`	`convertToRawTransformationMacro(String targetImageName, String sourceImageName, String inputElasticTransfFileName, String outputRawTransfFileName)` Method to convert an elastic deformation into raw format.
`static void`	`elasticTransformImageMacro(String targetImageName, String sourceImageName, String transformationFileName, String outputFileName)` Method to transform the source image given an elastic deformation.
`static void`	`evaluateImageSimilarity(String targetImageName, String sourceImageName)` Calculate image similarity between two images (target and source)
`static MainDialog`	`getMainDialog()` Get bUnwarpJ main dialog (if exists)
`static void`	`invertRawTransform(String inputTransfPath, String outputTransfPath, String targetTitle)` Approximate the inverse of a raw transform and save it to file.
`static void`	`loadElasticTransform(String transfPath, String targetTitle, String sourceTitle)` Load an elastic transform (bUnwarpJ format) from file and apply it to the source image.
`static void`	`loadLandmarks(String landmarksFilePath)` Load landmarks from file into existing source and target images.
`static void`	`loadRawTransform(String transfPath, String targetTitle, String sourceTitle)` Load a raw transform from file and apply it to the current source image.
`static void`	`loadSourceAffineMatrix(String affineMatrixPath)` Load an initial affine matrix for the source image.
`static void`	`loadSourceMask(String sourceMaskPath)` Load a source mask from file.
`static void`	`main(String[] args)` Main method for bUnwarpJ (command line).
`static void`	`rawTransformImageMacro(String targetImageName, String sourceImageName, String transformationFileName, String outputFileName)` Method to transform the source image given an raw deformation.
`void`	`run(String commandLine)` Method to lunch the plugin.
`static void`	`saveLandmarks(String landmarksFilePath)` Save landmarks to file.
`static void`	`showLandmarks()` Show landmark points in a results window.

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

- Constructor Detail
  - bUnwarpJ_
```
public bUnwarpJ_()
```
- Method Detail
  - run
```
public void run(String commandLine)
```
    Method to lunch the plugin.
    
    Specified by:
    
    run in interface ij.plugin.PlugIn
    
    Parameters:
    
    commandLine - command to determine the action
  - computeTransformationBatch
```
public static Transformation computeTransformationBatch(ij.ImagePlus targetImp,
                                                        ij.ImagePlus sourceImp,
                                                        ij.process.ImageProcessor targetMskIP,
                                                        ij.process.ImageProcessor sourceMskIP,
                                                        int mode,
                                                        int img_subsamp_fact,
                                                        int min_scale_deformation,
                                                        int max_scale_deformation,
                                                        double divWeight,
                                                        double curlWeight,
                                                        double landmarkWeight,
                                                        double imageWeight,
                                                        double consistencyWeight,
                                                        double stopThreshold)
```
    Method for images alignment with no graphical interface. This method gives as result a Transformation object that contains all the registration information.
    
    Parameters:
    
    targetImp - input target image
    
    sourceImp - input source image
    
    targetMskIP - target mask
    
    sourceMskIP - source mask
    
    mode - accuracy mode (0 - Fast, 1 - Accurate, 2 - Mono)
    
    img_subsamp_fact - image subsampling factor (from 0 to 7, representing 2^0=1 to 2^7 = 128)
    
    min_scale_deformation - (0 - Very Coarse, 1 - Coarse, 2 - Fine, 3 - Very Fine)
    
    max_scale_deformation - (0 - Very Coarse, 1 - Coarse, 2 - Fine, 3 - Very Fine, 4 - Super Fine)
    
    divWeight - divergence weight
    
    curlWeight - curl weight
    
    landmarkWeight - landmark weight
    
    imageWeight - image similarity weight
    
    consistencyWeight - consistency weight
    
    stopThreshold - stopping threshold
    
    Returns:
    
    results transformation object
  - computeTransformationBatch
```
public static Transformation computeTransformationBatch(ij.ImagePlus targetImp,
                                                        ij.ImagePlus sourceImp,
                                                        ij.process.ImageProcessor targetMskIP,
                                                        ij.process.ImageProcessor sourceMskIP,
                                                        Param parameter)
```
    Method for images alignment with no graphical interface. This method gives as result a Transformation object that contains all the registration information.
    
    Parameters:
    
    targetImp - input target image
    
    sourceImp - input source image
    
    targetMskIP - target mask
    
    sourceMskIP - source mask
    
    parameter - registration parameters
    
    Returns:
    
    results transformation object
  - computeTransformationBatch
```
public static Transformation computeTransformationBatch(ij.ImagePlus targetImp,
                                                        ij.ImagePlus sourceImp,
                                                        ij.process.ImageProcessor targetMskIP,
                                                        ij.process.ImageProcessor sourceMskIP,
                                                        AffineTransform targetAffineTransf,
                                                        AffineTransform sourceAffineTransf,
                                                        Param parameter)
```
    Method for images alignment with no graphical interface. This method gives as result a Transformation object that contains all the registration information.
    
    Parameters:
    
    targetImp - input target image
    
    sourceImp - input source image
    
    targetMskIP - target mask
    
    sourceMskIP - source mask
    
    targetAffineTransf - initial target affine transform
    
    sourceAffineTransf - initial source affine transform
    
    parameter - registration parameters
    
    Returns:
    
    results transformation object
  - computeTransformationBatch
```
public static Transformation computeTransformationBatch(int sourceWidth,
                                                        int sourceHeight,
                                                        int targetWidth,
                                                        int targetHeight,
                                                        Stack<Point> sourcePoints,
                                                        Stack<Point> targetPoints,
                                                        Param parameter)
```
    Method for images alignment with no graphical interface. This method gives as result a Transformation object that contains all the registration information.
    
    Parameters:
    
    sourceWidth -
    
    sourceHeight -
    
    targetWidth -
    
    targetHeight -
    
    sourcePoints -
    
    targetPoints -
    
    parameter - registration parameters
    
    Returns:
    
    results transformation object
  - alignImagesBatch
```
public static ij.ImagePlus[] alignImagesBatch(ij.ImagePlus targetImp,
                                              ij.ImagePlus sourceImp,
                                              ij.process.ImageProcessor targetMskIP,
                                              ij.process.ImageProcessor sourceMskIP,
                                              int mode,
                                              int img_subsamp_fact,
                                              int min_scale_deformation,
                                              int max_scale_deformation,
                                              double divWeight,
                                              double curlWeight,
                                              double landmarkWeight,
                                              double imageWeight,
                                              double consistencyWeight,
                                              double stopThreshold)
```
    Method for images alignment with no graphical interface. This method gives as result an array of 2 ImagePlus containing the source-target and target-source results respectively. Each of them has three slices: the final deformed image, its target image and its mask.
    
    Parameters:
    
    targetImp - input target image
    
    sourceImp - input source image
    
    targetMskIP - target mask
    
    sourceMskIP - source mask
    
    mode - accuracy mode (0 - Fast, 1 - Accurate, 2 - Mono)
    
    img_subsamp_fact - image subsampling factor (from 0 to 7, representing 2^0=1 to 2^7 = 128)
    
    min_scale_deformation - (0 - Very Coarse, 1 - Coarse, 2 - Fine, 3 - Very Fine)
    
    max_scale_deformation - (0 - Very Coarse, 1 - Coarse, 2 - Fine, 3 - Very Fine, 4 - Super Fine)
    
    divWeight - divergence weight
    
    curlWeight - curl weight
    
    landmarkWeight - landmark weight
    
    imageWeight - image similarity weight
    
    consistencyWeight - consistency weight
    
    stopThreshold - stopping threshold
    
    Returns:
    
    resulting ImagePlus array (with source-target and target-source results)
  - alignImagesBatch
```
public static ij.ImagePlus[] alignImagesBatch(ij.ImagePlus targetImp,
                                              ij.ImagePlus sourceImp,
                                              ij.process.ImageProcessor targetMskIP,
                                              ij.process.ImageProcessor sourceMskIP,
                                              Param parameter)
```
    Method for images alignment with no graphical interface. This method gives as result an array of 2 ImagePlus containing the source-target and target-source results respectively. Each of them has three slices: the final deformed image, its target image and its mask.
    
    Parameters:
    
    targetImp - input target image
    
    sourceImp - input source image
    
    targetMskIP - target mask
    
    sourceMskIP - source mask
    
    parameter - registration parameters
    
    Returns:
    
    resulting ImagePlus array (with source-target and target-source results)
  - alignImagesBatch
```
public static ij.ImagePlus[] alignImagesBatch(ij.ImagePlus targetImp,
                                              ij.ImagePlus sourceImp,
                                              ij.process.ImageProcessor targetMskIP,
                                              ij.process.ImageProcessor sourceMskIP,
                                              int mode,
                                              int img_subsamp_fact,
                                              int min_scale_deformation,
                                              int max_scale_deformation,
                                              double divWeight,
                                              double curlWeight,
                                              double landmarkWeight,
                                              double imageWeight,
                                              double consistencyWeight,
                                              double stopThreshold,
                                              double xScale,
                                              double yScale)
```
    Method for images alignment with no graphical interface. This method gives as result an array of 2 ImagePlus containing the source-target and target-source results (only final transformed image).
    
    Parameters:
    
    targetImp - input target image
    
    sourceImp - input source image
    
    targetMskIP - target mask
    
    sourceMskIP - source mask
    
    mode - accuracy mode (0 - Fast, 1 - Accurate, 2 - Mono)
    
    img_subsamp_fact - image subsampling factor (from 0 to 7, representing 2^0=1 to 2^7 = 128)
    
    min_scale_deformation - (0 - Very Coarse, 1 - Coarse, 2 - Fine, 3 - Very Fine)
    
    max_scale_deformation - (0 - Very Coarse, 1 - Coarse, 2 - Fine, 3 - Very Fine, 4 - Super Fine)
    
    divWeight - divergence weight
    
    curlWeight - curl weight
    
    landmarkWeight - landmark weight
    
    imageWeight - image similarity weight
    
    consistencyWeight - consistency weight
    
    stopThreshold - stopping threshold
    
    xScale - scale factor for x axis
    
    yScale - scale factor for y axis
    
    Returns:
    
    resulting ImagePlus array (with source-target and target-source results)
  - main
```
public static void main(String[] args)
```
    Main method for bUnwarpJ (command line).
    
    Parameters:
    
    args - arguments to decide the action
  - applyTransformToSource
```
public static void applyTransformToSource(String transfPath,
                                          ij.ImagePlus targetImp,
                                          ij.ImagePlus sourceImp)
```
    Apply transform loaded from file to source image (in place).
    
    Parameters:
    
    transfPath - complete path to transform file
    
    targetImp - target (fixed) image
    
    sourceImp - source (moving) image
  - elasticTransformImageMacro
```
public static void elasticTransformImageMacro(String targetImageName,
                                              String sourceImageName,
                                              String transformationFileName,
                                              String outputFileName)
```
    Method to transform the source image given an elastic deformation. To be called by the macro language instruction "call": http://rsb.info.nih.gov/ij/developer/macro/functions.html#call
    It calls the main command line method with the following option:
    -elastic_transform : TRANSFORM A SOURCE IMAGE WITH A GIVEN ELASTIC DEFORMATION
    target_image : In any image format
    source_image : In any image format
    transformation_file : As saved by bUnwarpJ in elastic format
    Output image : Output result in TIFF
    
    Parameters:
    
    targetImageName - target image file name (with path)
    
    sourceImageName - source image file name (with path)
    
    transformationFileName - transformation file name (with path)
    
    outputFileName - output file name (with path)
  - rawTransformImageMacro
```
public static void rawTransformImageMacro(String targetImageName,
                                          String sourceImageName,
                                          String transformationFileName,
                                          String outputFileName)
```
    Method to transform the source image given an raw deformation. To be called by the macro language instruction "call": http://rsb.info.nih.gov/ij/developer/macro/functions.html#call
    It calls the main command line method with the following option:
    -raw_transform : TRANSFORM A SOURCE IMAGE WITH A GIVEN RAW DEFORMATION
    target_image : In any image format
    source_image : In any image format
    transformation_file : As saved by bUnwarpJ in raw format
    Output image : Output result in TIFF
    
    Parameters:
    
    targetImageName - target image file name (with path)
    
    sourceImageName - source image file name (with path)
    
    transformationFileName - transformation file name (with path)
    
    outputFileName - output file name (with path)
  - compareElasticTransformationsMacro
```
public static void compareElasticTransformationsMacro(String targetImageName,
                                                      String sourceImageName,
                                                      String targetTransfFileName,
                                                      String sourceTransfFileName)
```
    Method to compare two opposite elastic transformations by warping index. To be called by the macro language instruction "call": http://rsb.info.nih.gov/ij/developer/macro/functions.html#call
    It calls the main command line method with the following option:
    -compare_elastic : COMPARE 2 OPPOSITE ELASTIC DEFORMATIONS (BY WARPING INDEX)
    target_image : In any image format
    source_image : In any image format
    target_transformation_file : As saved by bUnwarpJ
    source_transformation_file : As saved by bUnwarpJ
    
    Parameters:
    
    targetImageName - target image file name (with path)
    
    sourceImageName - source image file name (with path)
    
    targetTransfFileName - target transformation file name (with path)
    
    sourceTransfFileName - source transformation file name (with path)
  - compareElasticRawTransformationsMacro
```
public static void compareElasticRawTransformationsMacro(String targetImageName,
                                                         String sourceImageName,
                                                         String targetTransfFileName,
                                                         String sourceTransfFileName)
```
    Method to compare an elastic and a raw transformations by warping index. To be called by the macro language instruction "call": http://rsb.info.nih.gov/ij/developer/macro/functions.html#call
    It calls the main command line method with the following option:
    -compare_elastic_raw : COMPARE AN ELASTIC DEFORMATION WITH A RAW DEFORMATION (BY WARPING INDEX)
    target_image : In any image format
    source_image : In any image format
    target_transformation_file : As saved by bUnwarpJ
    source_transformation_file : As saved by bUnwarpJ
    
    Parameters:
    
    targetImageName - target image file name (with path)
    
    sourceImageName - source image file name (with path)
    
    targetTransfFileName - target transformation file name (with path)
    
    sourceTransfFileName - source transformation file name (with path)
  - compareRawTransformationsMacro
```
public static void compareRawTransformationsMacro(String targetImageName,
                                                  String sourceImageName,
                                                  String targetTransfFileName,
                                                  String sourceTransfFileName)
```
    Method to compare two raw transformations by warping index. To be called by the macro language instruction "call": http://rsb.info.nih.gov/ij/developer/macro/functions.html#call
    It calls the main command line method with the following option:
    -compare_raw : COMPARE 2 ELASTIC DEFORMATIONS (BY WARPING INDEX)
    target_image : In any image format
    source_image : In any image format
    Raw Transformation File 1 : As saved by bUnwarpJ in raw format
    Raw Transformation File 2 : As saved by bUnwarpJ in raw format
    
    Parameters:
    
    targetImageName - target image file name (with path)
    
    sourceImageName - source image file name (with path)
    
    targetTransfFileName - target transformation file name (with path)
    
    sourceTransfFileName - source transformation file name (with path)
  - convertToRawTransformationMacro
```
public static void convertToRawTransformationMacro(String targetImageName,
                                                   String sourceImageName,
                                                   String inputElasticTransfFileName,
                                                   String outputRawTransfFileName)
```
    Method to convert an elastic deformation into raw format. To be called by the macro language instruction "call": http://rsb.info.nih.gov/ij/developer/macro/functions.html#call
    It calls the main command line method with the following option:
    -convert_to_raw : CONVERT AN ELASTIC DEFORMATION INTO RAW FORMAT
    target_image : In any image format
    source_image : In any image format
    Input Elastic Transformation File : As saved by bUnwarpJ in elastic format
    Output Raw Transformation File : As saved by bUnwarpJ in raw format
    
    Parameters:
    
    targetImageName - target image file name (with path)
    
    sourceImageName - source image file name (with path)
    
    inputElasticTransfFileName - input transformation file name (with path)
    
    outputRawTransfFileName - output transformation file name (with path)
  - composeElasticTransformationsMacro
```
public static void composeElasticTransformationsMacro(String targetImageName,
                                                      String sourceImageName,
                                                      String inputElasticTransfFileName1,
                                                      String inputElasticTransfFileName2,
                                                      String outputRawTransfFileName)
```
    Method to compose two elastic transformations. To be called by the macro language instruction "call": http://rsb.info.nih.gov/ij/developer/macro/functions.html#call
    It calls the main command line method with the following option:
    -compose_elastic : COMPOSE TWO ELASTIC DEFORMATIONS
    target_image : In any image format
    source_image : In any image format
    Elastic Transformation File 1 : As saved by bUnwarpJ in elastic format
    Elastic Transformation File 2 : As saved by bUnwarpJ in elastic format
    Output Raw Transformation File : As saved by bUnwarpJ in raw format
    
    Parameters:
    
    targetImageName - target image file name (with path)
    
    sourceImageName - source image file name (with path)
    
    inputElasticTransfFileName1 - first input transformation file name (with path)
    
    inputElasticTransfFileName2 - second input transformation file name (with path)
    
    outputRawTransfFileName - output transformation file name (with path)
  - composeRawTransformationsMacro
```
public static void composeRawTransformationsMacro(String targetImageName,
                                                  String sourceImageName,
                                                  String inputRawTransfFileName1,
                                                  String inputRawTransfFileName2,
                                                  String outputRawTransfFileName)
```
    Method to compose two raw transformations. To be called by the macro language instruction "call": http://rsb.info.nih.gov/ij/developer/macro/functions.html#call
    It calls the main command line method with the following option:
    -compose_raw : COMPOSE TWO RAW DEFORMATIONS
    target_image : In any image format
    source_image : In any image format
    Raw Transformation File 1 : As saved by bUnwarpJ in raw format
    Raw Transformation File 2 : As saved by bUnwarpJ in raw format
    Output Raw Transformation File : As saved by bUnwarpJ in raw format
    
    Parameters:
    
    targetImageName - target image file name (with path)
    
    sourceImageName - source image file name (with path)
    
    inputRawTransfFileName1 - first input transformation file name (with path)
    
    inputRawTransfFileName2 - second input transformation file name (with path)
    
    outputRawTransfFileName - output transformation file name (with path)
  - composeRawElasticTransformationsMacro
```
public static void composeRawElasticTransformationsMacro(String targetImageName,
                                                         String sourceImageName,
                                                         String inputRawTransfFileName,
                                                         String inputElasticTransfFileName,
                                                         String outputRawTransfFileName)
```
    Method to compose a raw transformation with an elastic transformation. To be called by the macro language instruction "call": http://rsb.info.nih.gov/ij/developer/macro/functions.html#call
    It calls the main command line method with the following option:
    -compose_raw_elastic : COMPOSE A RAW DEFORMATION WITH AN ELASTIC DEFORMATION
    target_image : In any image format
    source_image : In any image format
    Raw Transformation File : As saved by bUnwarpJ in raw format
    Elastic Transformation File : As saved by bUnwarpJ in elastic format
    Output Raw Transformation File : As saved by bUnwarpJ in raw format
    
    Parameters:
    
    targetImageName - target image file name (with path)
    
    sourceImageName - source image file name (with path)
    
    inputRawTransfFileName - input raw transformation file name (with path)
    
    inputElasticTransfFileName - input elastic transformation file name (with path)
    
    outputRawTransfFileName - output transformation file name (with path)
  - adaptCoefficientsMacro
```
public static void adaptCoefficientsMacro(String targetImageName,
                                          String sourceImageName,
                                          String inputElasticTransfFileName,
                                          String outputElasticTransfFileName,
                                          String sizeFactor)
```
    Method to adapt an elastic transformation given a new image size. To be called by the macro language instruction "call": http://rsb.info.nih.gov/ij/developer/macro/functions.html#call
    It calls the main command line method with the following option:
    -adapt_transform : ADAPT AN ELASTIC DEFORMATION GIVEN A NEW IMAGE SIZE
    target_image : In any image format
    source_image : In any image format
    Input Elastic Transformation File : As saved by bUnwarpJ in elastic format
    Output Elastic Transformation File : As saved by bUnwarpJ in elastic format
    Image Size Factor : Double (0.25, 0.5, 2, 4, 8...)
    
    Parameters:
    
    targetImageName - target image file name (with path)
    
    sourceImageName - source image file name (with path)
    
    inputElasticTransfFileName - input elastic transformation file name (with path)
    
    outputElasticTransfFileName - output elastic transformation file name (with path)
    
    sizeFactor - double size factor (between old and new image)
  - evaluateImageSimilarity
```
public static void evaluateImageSimilarity(String targetImageName,
                                           String sourceImageName)
```
    Calculate image similarity between two images (target and source)
    
    Parameters:
    
    targetImageName - name of the target image
    
    sourceImageName - name of the source image
  - loadLandmarks
```
public static void loadLandmarks(String landmarksFilePath)
```
    Load landmarks from file into existing source and target images. Therefore, a bUnwarpJ dialog must exist.
    
    Parameters:
    
    landmarksFilePath - complete path to landmarks file
  - saveLandmarks
```
public static void saveLandmarks(String landmarksFilePath)
```
    Save landmarks to file. Therefore, a bUnwarpJ dialog must exist.
    
    Parameters:
    
    landmarksFilePath - complete path to output landmark file
  - showLandmarks
```
public static void showLandmarks()
```
    Show landmark points in a results window.
  - loadElasticTransform
```
public static void loadElasticTransform(String transfPath,
                                        String targetTitle,
                                        String sourceTitle)
```
    Load an elastic transform (bUnwarpJ format) from file and apply it to the source image.
    
    Parameters:
    
    transfPath - complete path to elastic transform file
    
    targetTitle - title of the target image
    
    sourceTitle - title of the source image
  - loadRawTransform
```
public static void loadRawTransform(String transfPath,
                                    String targetTitle,
                                    String sourceTitle)
```
    Load a raw transform from file and apply it to the current source image.
    
    Parameters:
    
    transfPath - complete path to raw transform file
    
    targetTitle - title of the target image
    
    sourceTitle - title of the source image
  - applyRawTransformToSource
```
public static void applyRawTransformToSource(String transfPath,
                                             ij.ImagePlus targetImp,
                                             ij.ImagePlus sourceImp)
```
    Apply a raw transform loaded from file to the source image.
    
    Parameters:
    
    transfPath - complete path to raw transform file
    
    targetImp - target image
    
    sourceImp - source image
  - compareOppositeElasticTransforms
```
public static void compareOppositeElasticTransforms(String directTransfPath,
                                                    String inverseTransfPath,
                                                    String targetTitle,
                                                    String sourceTitle)
```
    Compare opposite elastic transforms loaded from file. The result is expressed using the warping index and displayed in the Log window.
    
    Parameters:
    
    directTransfPath - complete path to direct elastic transform file
    
    inverseTransfPath - complete path to inverse elastic transform file
    
    targetTitle - title of the target image
    
    sourceTitle - title of the source image
  - compareElasticRawTransforms
```
public static void compareElasticRawTransforms(String elasticTransfPath,
                                               String rawTransfPath,
                                               String targetTitle,
                                               String sourceTitle)
```
    Compare an elastic and a raw transform loaded from file. The result is expressed using the warping index and displayed in the Log window.
    
    Parameters:
    
    elasticTransfPath - complete path to elastic transform file
    
    rawTransfPath - complete path to raw transform file
    
    targetTitle - target image title
    
    sourceTitle - source image title
  - compareRawTransforms
```
public static void compareRawTransforms(String rawTransfPath1,
                                        String rawTransfPath2,
                                        String targetTitle,
                                        String sourceTitle)
```
    Compare two raw transforms loaded from file. The result is expressed using the warping index and displayed in the Log window. Both transforms have the same direction.
    
    Parameters:
    
    rawTransfPath1 - complete path to first raw transform file
    
    rawTransfPath2 - complete path to second raw transform file
    
    targetTitle - title of the target image
    
    sourceTitle - title of the source image
  - convertToRaw
```
public static void convertToRaw(String elasticTransfPath,
                                String rawTransfPath,
                                String targetTitle)
```
    Convert an elastic transform to raw format and save it to file.
    
    Parameters:
    
    elasticTransfPath - complete path to input elastic transform file
    
    rawTransfPath - complete path to output raw transform file
    
    targetTitle - title of the target image
  - convertToElastic
```
public static void convertToElastic(String rawTransfPath,
                                    String elasticTransfPath,
                                    String strIntervals,
                                    String targetTitle)
```
    Convert an elastic transform to raw format and save it to file.
    
    Parameters:
    
    rawTransfPath - complete path to input raw transform file
    
    elasticTransfPath - complete path to output elastic transform file
    
    strIntervals - number of intervals in the B-spline grid
    
    targetTitle - title of the target image
  - composeElasticTransforms
```
public static void composeElasticTransforms(String elasticTransfPath1,
                                            String elasticTransfPath2,
                                            String rawTransfPath,
                                            String targetTitle)
```
    Compose two elastic transforms into a raw transform.
    
    Parameters:
    
    elasticTransfPath1 - complete path to first elastic transform file
    
    elasticTransfPath2 - complete path to second elastic transform file
    
    rawTransfPath - complete path to output raw transform file
    
    targetTitle - title of the target image
  - composeRawTransforms
```
public static void composeRawTransforms(String rawTransfPath1,
                                        String rawTransfPath2,
                                        String outputRawTransfPath,
                                        String targetTitle)
```
    Compose two raw transforms into another raw transform.
    
    Parameters:
    
    rawTransfPath1 - complete path to first raw transform file
    
    rawTransfPath2 - complete path to second raw transform file
    
    outputRawTransfPath - complete path to output raw transform file
    
    targetTitle - title of the target image
  - composeRawElasticTransforms
```
public static void composeRawElasticTransforms(String rawTransfPath,
                                               String elasticTransfPath,
                                               String outputRawTransfPath,
                                               String targetTitle,
                                               String sourceTitle)
```
    Compose two a raw and an elastic transform into a raw transform.
    
    Parameters:
    
    rawTransfPath - complete path to raw transform file
    
    elasticTransfPath - complete path to elastic transform file
    
    outputRawTransfPath - complete path to output raw transform file
    
    targetTitle - title of the target image
    
    sourceTitle - title of the source image
  - adaptCoefficients
```
public static void adaptCoefficients(String inputTransfPath,
                                     String strImageFactor,
                                     String outputTransfPath)
```
    Adapt the B-spline coefficients to a new image size.
    
    Parameters:
    
    inputTransfPath - complete path to input transform file
    
    strImageFactor - string containing the image factor to apply
    
    outputTransfPath - complete path to output transform file
  - loadSourceMask
```
public static void loadSourceMask(String sourceMaskPath)
```
    Load a source mask from file.
    
    Parameters:
    
    sourceMaskPath - complete path to source mask image
  - loadSourceAffineMatrix
```
public static void loadSourceAffineMatrix(String affineMatrixPath)
```
    Load an initial affine matrix for the source image.
    
    Parameters:
    
    affineMatrixPath - complete path to affine matrix file.
  - invertRawTransform
```
public static void invertRawTransform(String inputTransfPath,
                                      String outputTransfPath,
                                      String targetTitle)
```
    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 raw transform file
    
    targetTitle - target image title
  - getMainDialog
```
public static MainDialog getMainDialog()
```
    Get bUnwarpJ main dialog (if exists)
    
    Returns:
    
    bUnwarpJ main dialog or null if it does not exist

Class bUnwarpJ_

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

bUnwarpJ_

Method Detail

run

computeTransformationBatch

computeTransformationBatch

computeTransformationBatch

computeTransformationBatch

alignImagesBatch

alignImagesBatch

alignImagesBatch

main

applyTransformToSource

elasticTransformImageMacro

rawTransformImageMacro

compareElasticTransformationsMacro

compareElasticRawTransformationsMacro

compareRawTransformationsMacro

convertToRawTransformationMacro

composeElasticTransformationsMacro

composeRawTransformationsMacro

composeRawElasticTransformationsMacro

adaptCoefficientsMacro

evaluateImageSimilarity

loadLandmarks

saveLandmarks

showLandmarks

loadElasticTransform

loadRawTransform

applyRawTransformToSource

compareOppositeElasticTransforms

compareElasticRawTransforms

compareRawTransforms

convertToRaw

convertToElastic

composeElasticTransforms

composeRawTransforms

composeRawElasticTransforms

adaptCoefficients

loadSourceMask

loadSourceAffineMatrix

invertRawTransform

getMainDialog