- ACCURATE_MODE - Static variable in class bunwarpj.MainDialog
-
accurate mode constant
- actionPerformed(ActionEvent) - Method in class bunwarpj.ClearAll
-
Actions to take place with the dialog for clearing everything
- actionPerformed(ActionEvent) - Method in class bunwarpj.IODialog
-
Actions to be taking during the dialog.
- actionPerformed(ActionEvent) - Method in class bunwarpj.MainDialog
-
Actions to be taken during the dialog.
- ADAPT_COEFFICIENTS - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to adapt B-spline coefficients to a scale
- adaptCoefficients(String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Adapt the B-spline coefficients to a new image size.
- adaptCoefficients(String, double, String) - Static method in class bunwarpj.MiscTools
-
Adapt B-spline coefficients based on a scale factor.
- adaptCoefficients(double, double, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Adapt B-spline coefficients to a scale factor
- adaptCoefficientsMacro(String, String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Method to adapt an elastic transformation given a new image size.
- ADD_CROSS - Static variable in class bunwarpj.PointAction
-
constant to identify the add cross tool
- addMaskPoint(int, int) - Method in class bunwarpj.PointHandler
-
Add a point to the mask.
- addPoint(int, int) - Method in class bunwarpj.PointHandler
-
Add a point to the list of points.
- addWorkload(int) - Static method in class bunwarpj.ProgressBar
-
Extend the amount of work to perform by batch.
- alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, int, int, int, int, double, double, double, double, double, double) - Static method in class bunwarpj.bUnwarpJ_
-
Method for images alignment with no graphical interface.
- alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, Param) - Static method in class bunwarpj.bUnwarpJ_
-
Method for images alignment with no graphical interface.
- alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, int, int, int, int, double, double, double, double, double, double, double, double) - Static method in class bunwarpj.bUnwarpJ_
-
Method for images alignment with no graphical interface.
- antiSymmetricPadding(double[][], int) - Static method in class bunwarpj.MathTools
-
- antiSymmetricPadding(double[], int, int) - Static method in class bunwarpj.MathTools
-
- antiSymmetricPadding(float[], int, int) - Static method in class bunwarpj.MathTools
-
- applyRawTransformationToSource(double[][], double[][]) - Method in class bunwarpj.MainDialog
-
Apply a raw transformation to the source image.
- applyRawTransformationToSource(ImagePlus, ImagePlus, BSplineModel, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Apply a given raw transformation to the source image.
- applyRawTransformToSource(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.bUnwarpJ_
-
Apply a raw transform loaded from file to the source image.
- applyTransformationMT(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Apply a given B-spline transformation to the source (gray-scale) image.
- applyTransformationToSource(int, double[][], double[][]) - Method in class bunwarpj.MainDialog
-
Apply the transformation defined by the spline coefficients to the source
image.
- applyTransformationToSource(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Deprecated.
- applyTransformationToSource(ImagePlus, ImagePlus, BSplineModel, BSplineModel, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Deprecated.
- applyTransformationToSourceMT(ImagePlus, ImagePlus, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Apply a given B-spline transformation to the source (gray-scale) image.
- applyTransformationToSourceMT(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Apply a given B-spline transformation to the source (gray-scale) image.
- applyTransformToSource(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.bUnwarpJ_
-
Apply transform loaded from file to source image (in place).
- applyTransformToStack(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.MiscTools
-
Apply transform saved on a file to all slices of moving image
- approximateInverseCoords(double[], ImagePlus, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Approximate the transformed coordinates of a point from the
moving image into the fixed image.
- canAddMaskPoints() - Method in class bunwarpj.PointHandler
-
Check if it is possible to add points to the mask.
- ClearAll - Class in bunwarpj
-
Class to clear all the processes and actions in bUnwarpJ.
- clearMask() - Method in class bunwarpj.Mask
-
Set to true every pixel of the full-size mask.
- clearMask() - Method in class bunwarpj.PointHandler
-
Remove all the elements of the mask.
- clearPyramids() - Method in class bunwarpj.BSplineModel
-
Clear the pyramid.
- closeMask(int) - Method in class bunwarpj.PointHandler
-
Close mask.
- COMPARE_ELASTIC_RAW - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to compare elastic and raw transforms
- COMPARE_OPPOSITE_ELASTIC - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to compare opposite elastic transforms
- COMPARE_RAW - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to compare raw transforms
- compareElasticRawTransformationsMacro(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Method to compare an elastic and a raw transformations by warping index.
- compareElasticRawTransforms(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Compare an elastic and a raw transform loaded from file.
- compareElasticTransformationsMacro(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Method to compare two opposite elastic transformations by warping index.
- compareOppositeElasticTransforms(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Compare opposite elastic transforms loaded from file.
- compareRawTransformationsMacro(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Method to compare two raw transformations by warping index.
- compareRawTransforms(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Compare two raw transforms loaded from file.
- COMPOSE_ELASTIC - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to compose elastic transforms
- COMPOSE_RAW - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to compose raw transforms
- COMPOSE_RAW_ELASTIC - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to compose raw and elastic transforms
- composeElasticTransformations(ImagePlus, int, double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Compose two elastic deformations into a raw deformation.
- composeElasticTransformationsAtPixelLevel(ImagePlus, int, double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Compose two elastic deformations into a raw deformation at pixel level.
- composeElasticTransformationsMacro(String, String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Method to compose two elastic transformations.
- composeElasticTransforms(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Compose two elastic transforms into a raw transform.
- composeElasticTransforms(String, String, String, ImagePlus) - Static method in class bunwarpj.MiscTools
-
Compose two elastic transform into a raw transform and save it to file
- composeRawElasticTransformations(ImagePlus, int, double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Compose a raw deformation and an elastic deformation into a raw deformation.
- composeRawElasticTransformationsMacro(String, String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Method to compose a raw transformation with an elastic transformation.
- composeRawElasticTransforms(String, String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Compose two a raw and an elastic transform into a raw transform.
- composeRawElasticTransforms(String, String, String, ImagePlus, ImagePlus) - Static method in class bunwarpj.MiscTools
-
Compose a raw and an elastic transform and save result into file.
- composeRawTransformations(int, int, double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Compose two raw transformations (Bilinear interpolation)
- composeRawTransformationsMacro(String, String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Method to compose two raw transformations.
- composeRawTransforms(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Compose two raw transforms into another raw transform.
- composeRawTransforms(String, String, String, ImagePlus) - Static method in class bunwarpj.MiscTools
-
Compose raw transforms into another raw transform and save to file.
- computeTransformationBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, int, int, int, int, double, double, double, double, double, double) - Static method in class bunwarpj.bUnwarpJ_
-
Method for images alignment with no graphical interface.
- computeTransformationBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, Param) - Static method in class bunwarpj.bUnwarpJ_
-
Method for images alignment with no graphical interface.
- computeTransformationBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, AffineTransform, AffineTransform, Param) - Static method in class bunwarpj.bUnwarpJ_
-
Method for images alignment with no graphical interface.
- computeTransformationBatch(int, int, int, int, Stack<Point>, Stack<Point>, Param) - Static method in class bunwarpj.bUnwarpJ_
-
Method for images alignment with no graphical interface.
- consistencyWeight - Variable in class bunwarpj.Param
-
consistency weight
- CONVERT_TO_ELASTIC - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to convert raw transform to B-spline format
- CONVERT_TO_RAW - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to convert elastic transform to raw format
- convertElasticTransformationToRaw(ImagePlus, int, double[][], double[][], double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Calculate the raw transformation mapping from B-spline
coefficients.
- convertRawTransformationToBSpline(ImagePlus, int, double[][], double[][], double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Convert the raw transformation mapping to B-spline
coefficients.
- convertToElastic(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Convert an elastic transform to raw format and save it to file.
- convertToInterpCoef(double[], double[], double) - Static method in class math.BSpline
-
Convert to interpolation coefficients
- convertToRaw(String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Convert an elastic transform to raw format and save it to file.
- convertToRawTransformationMacro(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Method to convert an elastic deformation into raw format.
- convertToSamples(double[], double[]) - Static method in class math.BSpline
-
Convert the spline coefficients to samples
- createDownsampled(ImageProcessor, float, float, float) - Static method in class bunwarpj.MiscTools
-
Create a downsampled ImageProcessor.
- Credits - Class in bunwarpj
-
Class to show the bUnwarpJ credits
- Credits() - Constructor for class bunwarpj.Credits
-
- CumulativeQueue - Class in bunwarpj
-
Class to create a cumulative queue in bUnwarpJ.
- CumulativeQueue(int) - Constructor for class bunwarpj.CumulativeQueue
-
Create a new instance of CumulativeQueue.
- curlWeight - Variable in class bunwarpj.Param
-
curl weight
- currentSize() - Method in class bunwarpj.CumulativeQueue
-
Get the current size of the queue.
- getAnisotropyCorrection() - Method in class bunwarpj.Param
-
- getCoefficients() - Method in class bunwarpj.BSplineModel
-
Get b-spline coefficients.
- getCurrentDepth() - Method in class bunwarpj.BSplineModel
-
Get current depth.
- getCurrentHeight() - Method in class bunwarpj.BSplineModel
-
Get current height.
- getCurrentImage() - Method in class bunwarpj.BSplineModel
-
Get current image.
- getCurrentPoint() - Method in class bunwarpj.PointHandler
-
Get current point index.
- getCurrentTool() - Method in class bunwarpj.PointToolbar
-
Get current tool.
- getCurrentWidth() - Method in class bunwarpj.BSplineModel
-
Get current width.
- getDeformation(double[][], double[][], boolean) - Method in class bunwarpj.Transformation
-
Get the deformation from the corresponding coefficients.
- getDirectDeformationCoefficientsX() - Method in class bunwarpj.Transformation
-
Get the direct deformation X coefficients.
- getDirectDeformationCoefficientsY() - Method in class bunwarpj.Transformation
-
Get the direct deformation Y coefficients.
- getDirectResults() - Method in class bunwarpj.Transformation
-
Get direct results window
- getFactorHeight() - Method in class bunwarpj.BSplineModel
-
Get factor height.
- getFactorWidth() - Method in class bunwarpj.BSplineModel
-
Get fact or width.
- getHeight() - Method in class bunwarpj.BSplineModel
-
Get height.
- getImage() - Method in class bunwarpj.BSplineModel
-
Get image (at the maximum resolution size determined by the scaling).
- getInsets() - Method in class bunwarpj.ClearAll
-
Get the insets
- getInsets() - Method in class bunwarpj.IODialog
-
Get the insets.
- getIntervals() - Method in class bunwarpj.Transformation
-
Get the current number of intervals between B-spline coefficients.
- getInverseDeformationCoefficientsX() - Method in class bunwarpj.Transformation
-
Get the inverse deformation X coefficients.
- getInverseDeformationCoefficientsY() - Method in class bunwarpj.Transformation
-
Get the inverse deformation Y coefficients.
- getInverseResults() - Method in class bunwarpj.Transformation
-
Get inverse results window
- getMacroArgs() - Method in class bunwarpj.MainDialog
-
Get arguments from the macro call
- getMainDialog() - Static method in class bunwarpj.bUnwarpJ_
-
Get bUnwarpJ main dialog (if exists)
- getOriginalImage() - Method in class bunwarpj.BSplineModel
-
Get original image.
- getOriginalImageHeight() - Method in class bunwarpj.BSplineModel
-
Get original image height.
- getOriginalImageWidth() - Method in class bunwarpj.BSplineModel
-
Get original image width.
- getOriginalSourceIP() - Method in class bunwarpj.MainDialog
-
Get original source image processor.
- getOriginalTargetIP() - Method in class bunwarpj.MainDialog
-
Get original target image processor.
- getPixelValFromPyramid(int, int) - Method in class bunwarpj.BSplineModel
-
Get the pixel value from the image pyramid.
- getPoint(int) - Method in class bunwarpj.Mask
-
Get a point from the mask.
- getPoint() - Method in class bunwarpj.PointHandler
-
Get the current point in the list of points.
- getPointAction() - Method in class bunwarpj.PointHandler
-
Get point action.
- getPoints() - Method in class bunwarpj.PointHandler
-
Get the list of points.
- getPyramidDepth() - Method in class bunwarpj.BSplineModel
-
Get pyramid depth.
- getScaleCorrection() - Method in class bunwarpj.Param
-
- getShearCorrection() - Method in class bunwarpj.Param
-
- getSmallestHeight() - Method in class bunwarpj.BSplineModel
-
Get smallest height.
- getSmallestWidth() - Method in class bunwarpj.BSplineModel
-
Get smallest width.
- getSource() - Method in class bunwarpj.MainDialog
-
Get source image model.
- getSourceAffineMatrix() - Method in class bunwarpj.MainDialog
-
Get the source initial affine matrix.
- getSourceImp() - Method in class bunwarpj.MainDialog
-
Get reference to source image
- getSourceMask() - Method in class bunwarpj.MainDialog
-
Get source Mask.
- getSourceMsk() - Method in class bunwarpj.MainDialog
-
Get source mask.
- getSourcePh() - Method in class bunwarpj.MainDialog
-
Get source point handler.
- getSubImage() - Method in class bunwarpj.BSplineModel
-
Get subsampled output image.
- getSubsamplingFactor() - Method in class bunwarpj.BSplineModel
-
Get sub-sampling factor at highest resolution
- getSum() - Method in class bunwarpj.CumulativeQueue
-
Get the sum of the queue.
- getTarget() - Method in class bunwarpj.MainDialog
-
Get target image model.
- getTargetAffineMatrix() - Method in class bunwarpj.MainDialog
-
Get the target initial affine matrix.
- getTargetImp() - Method in class bunwarpj.MainDialog
-
Get reference to target image
- getTargetMask() - Method in class bunwarpj.MainDialog
-
Get target Mask.
- getTargetMsk() - Method in class bunwarpj.MainDialog
-
Get target mask.
- getTargetPh() - Method in class bunwarpj.MainDialog
-
Get target point handler.
- getThread() - Method in class bunwarpj.BSplineModel
-
Get thread.
- getThread() - Method in class bunwarpj.FinalAction
-
Get the thread.
- getUserSelectedFilePath(String, boolean) - Static method in class bunwarpj.MiscTools
-
Show a non-recordable dialog so the user selects a file.
- getValue(double, double) - Method in class bunwarpj.Mask
-
Get the value of the mask at a certain pixel.
- getWeightDx(int, int) - Method in class bunwarpj.BSplineModel
-
Get weight dx.
- getWeightDxDx(int, int) - Method in class bunwarpj.BSplineModel
-
Get weight dxdx.
- getWeightDxDy(int, int) - Method in class bunwarpj.BSplineModel
-
Get weight dxdy.
- getWeightDy(int, int) - Method in class bunwarpj.BSplineModel
-
Get weight dy.
- getWeightDyDy(int, int) - Method in class bunwarpj.BSplineModel
-
Get weight dydy.
- getWeightI(int, int) - Method in class bunwarpj.BSplineModel
-
Get image coefficient weight.
- getWidth() - Method in class bunwarpj.BSplineModel
-
Get width.
- grayImage(PointHandler) - Method in class bunwarpj.MainDialog
-
Method to color the area of the mask.
- imageSimilarity(ImagePlus, ImagePlus, Mask, boolean) - Static method in class bunwarpj.MiscTools
-
Calculate image similarity between two images (target and source)
- imageWeight - Variable in class bunwarpj.Param
-
image similarity weight
- img_subsamp_fact - Variable in class bunwarpj.Param
-
image subsampling factor (from 0 to 7, representing 2^0=1 to 2^7 = 128)
- initialAntiCausalCoefficient(double[], double) - Static method in class math.BSpline
-
Get initial anti-causal coefficients
- initialCausalCoefficient(double[], double, double) - Static method in class math.BSpline
-
Initialization of causal coefficients for mirror boundary conditions
- initializeOutputIPs() - Method in class bunwarpj.FinalAction
-
Initialize output image plus
- integAS(double[]) - Static method in class math.BSpline
-
Begin computation of the running sums.
- integSA(double[], double[]) - Static method in class math.BSpline
-
Begin computation of the running sums.
- interpolateD(double[]) - Method in class bunwarpj.BSplineModel
-
Interpolate the X and Y derivatives of the image at a
given point.
- interpolateD2(double[]) - Method in class bunwarpj.BSplineModel
-
Interpolate the XY, XX and YY derivatives of the image at a
given point.
- interpolateDx() - Method in class bunwarpj.BSplineModel
-
Interpolate the X derivative of the image at a given point.
- interpolateDxDx() - Method in class bunwarpj.BSplineModel
-
Interpolate the X derivative of the image at a given point.
- interpolateDxDy() - Method in class bunwarpj.BSplineModel
-
Interpolate the X derivative of the image at a given point.
- interpolateDy() - Method in class bunwarpj.BSplineModel
-
Interpolate the Y derivative of the image at a given point.
- interpolateDyDy() - Method in class bunwarpj.BSplineModel
-
Interpolate the X derivative of the image at a given point.
- interpolateI() - Method in class bunwarpj.BSplineModel
-
Interpolate the image at a given point.
- INVERT_RAW - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to invert a raw transform
- INVERTMASK - Static variable in class bunwarpj.PointAction
-
constant to identify the outer mask tool
- invertMatrixSVD(int, int, double[][], double[][]) - Static method in class bunwarpj.MathTools
-
Invert a matrix by the Singular Value Decomposition method.
- invertRawTransform(String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Approximate the inverse of a raw transform and save it to file.
- invertRawTransformation(ImagePlus, double[][], double[][], double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
- invertRawTransformation(String, String, ImagePlus) - Static method in class bunwarpj.MiscTools
-
Approximate the inverse of a raw transform and save it to file.
- IODialog - Class in bunwarpj
-
Class to create the Input/Output dialog to deal with the files
to keep the information of bUnwarpJ.
- IODialog(Frame, ImagePlus, ImagePlus, PointHandler, PointHandler, MainDialog) - Constructor for class bunwarpj.IODialog
-
Create a new instance of IODialog.
- isClearMaskSet() - Method in class bunwarpj.MainDialog
-
Get clearMask flag.
- isFinalActionLaunched() - Method in class bunwarpj.MainDialog
-
Get finalActionLaunched flag.
- isFinest() - Method in class bunwarpj.BSplineModel
-
Check if the coefficients pyramid is empty.
- isFromStack() - Method in class bunwarpj.Mask
-
Check if the mask was taken from the stack.
- isMacroCall() - Method in class bunwarpj.MainDialog
-
Get the macro flag
- isSaveTransformationSet() - Method in class bunwarpj.MainDialog
-
Get saveTransformation flag.
- isStopRegistrationSet() - Method in class bunwarpj.MainDialog
-
Get stopRegistration flag.
- itemStateChanged(ItemEvent) - Method in class bunwarpj.MainDialog
-
Action to be taken when choices change.
- landmarkWeight - Variable in class bunwarpj.Param
-
landmark weight
- linearLeastSquares(double[][], double[]) - Static method in class bunwarpj.MathTools
-
Gives the least-squares solution to (A * x = b) such that
(A^T * A)^-1 * A^T * b = x is a vector of size (column), where A is
a (line x column) matrix, and where b is a vector of size (line).
- LOAD_ELASTIC_TRANSF - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to load an elastic transform
- LOAD_LANDMARKS - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to load landmarks from file
- LOAD_RAW_TRANSF - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to load a raw transform
- LOAD_SOURCE_AFFINE - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to load an affine matrix to the source image
- LOAD_SOURCE_MASK - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to load a source mask
- loadAffineMatrix(String, double[][]) - Static method in class bunwarpj.MiscTools
-
Load an affine matrix from a file.
- loadDirectTransformation(String) - Method in class bunwarpj.Transformation
-
Load target to source transformation from a file.
- loadElasticTransform(String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Load an elastic transform (bUnwarpJ format) from file and apply it to
the source image.
- loadInverseTransformation(String) - Method in class bunwarpj.Transformation
-
Load source to target transformation from a file.
- loadLandmarks(String) - Static method in class bunwarpj.bUnwarpJ_
-
Load landmarks from file into existing source and target images.
- loadPointRoiAsLandmarks(ImagePlus, ImagePlus, Stack<Point>, Stack<Point>) - Static method in class bunwarpj.MiscTools
-
Load point rois in the source and target images as landmarks.
- loadPoints(String, Stack<Point>, Stack<Point>) - Static method in class bunwarpj.MiscTools
-
Load landmarks from file.
- loadRawTransform(String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Load a raw transform from file and apply it to the current source image.
- loadRawTransformation(String, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Load a raw transformation from a file.
- loadRawTransformation(String, double[], double[]) - Static method in class bunwarpj.MiscTools
-
Load a raw transformation from a file.
- loadSourceAffineMatrix(String) - Static method in class bunwarpj.bUnwarpJ_
-
Load an initial affine matrix for the source image.
- loadSourceMask(String) - Static method in class bunwarpj.bUnwarpJ_
-
Load a source mask from file.
- loadTransformation(String, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Load a transformation from a file.
- MAGNIFIER - Static variable in class bunwarpj.PointAction
-
constant to identify the magnifier tool
- main(String[]) - Static method in class bunwarpj.bUnwarpJ_
-
Main method for bUnwarpJ (command line).
- MainDialog - Class in bunwarpj
-
Class to create the dialog for bUnwarpJ.
- MainDialog(Frame, ImagePlus[], int, int, int, int, double, double, double, double, double, double, boolean, boolean) - Constructor for class bunwarpj.MainDialog
-
Create a new instance of MainDialog.
- makeAffineMatrix(double, double, double, double, double, double, double) - Static method in class bunwarpj.Transformation
-
Makes an affine transformation matrix from the given scale, shear,
rotation and translation values
if you want a uniquely retrievable matrix, give sheary=0
- Mask - Class in bunwarpj
-
This class is responsible for the mask preprocessing that takes
place concurrently with user-interface events.
- Mask(ImageProcessor, boolean) - Constructor for class bunwarpj.Mask
-
Constructor, the input image is used only to take the
image size if take_mask is false, otherwise, it is used as the
mask information.
- Mask(int, int) - Constructor for class bunwarpj.Mask
-
Create mask of specific size (all pixels set to true)
- MASK - Static variable in class bunwarpj.PointAction
-
constant to identify the inner mask tool
- math - package math
-
- MathTools - Class in bunwarpj
-
This class has the math methods to deal with b-splines and images.
- MathTools() - Constructor for class bunwarpj.MathTools
-
- MAX_OUTPUT_SIZE - Static variable in class bunwarpj.BSplineModel
-
maximum output window dimensions
- max_scale_deformation - Variable in class bunwarpj.Param
-
maximum scale deformation (0 - Very Coarse, 1 - Coarse, 2 - Fine, 3 - Very Fine, 4 - Super Fine)
- mean(double[]) - Static method in class math.BSpline
-
Calculate mean value on the period (2*length(A)-2)
- min_scale_deformation - Variable in class bunwarpj.Param
-
minimum scale deformation (0 - Very Coarse, 1 - Coarse, 2 - Fine, 3 - Very Fine)
- MiscTools - Class in bunwarpj
-
Different tools for the bUnwarpJ interface.
- MiscTools() - Constructor for class bunwarpj.MiscTools
-
- mode - Variable in class bunwarpj.Param
-
mode accuracy mode (0 - Fast, 1 - Accurate, 2 - Mono)
- MONO_MODE - Static variable in class bunwarpj.MainDialog
-
unidirectional ("mono") mode constant
- mouseClicked(MouseEvent) - Method in class bunwarpj.PointAction
-
Method mouse clicked.
- mouseClicked(MouseEvent) - Method in class bunwarpj.PointToolbar
-
Mouse clicked.
- mouseDragged(MouseEvent) - Method in class bunwarpj.PointAction
-
Method mouse dragged, applied move the cross.
- mouseEntered(MouseEvent) - Method in class bunwarpj.PointAction
-
Method mouse entered, applied to set the main window.
- mouseEntered(MouseEvent) - Method in class bunwarpj.PointToolbar
-
Mouse entered.
- mouseExited(MouseEvent) - Method in class bunwarpj.PointAction
-
Method mouse exited.
- mouseExited(MouseEvent) - Method in class bunwarpj.PointToolbar
-
Mouse exited.
- mouseMoved(MouseEvent) - Method in class bunwarpj.PointAction
-
Method mouse moved, show the coordinates of the mouse pointer.
- mousePressed(MouseEvent) - Method in class bunwarpj.PointAction
-
Method mouse pressed, allow all the different option over the images.
- mousePressed(MouseEvent) - Method in class bunwarpj.PointToolbar
-
Mouse pressed, applied to select the tool.
- mouseReleased(MouseEvent) - Method in class bunwarpj.PointAction
-
Method mouse released.
- mouseReleased(MouseEvent) - Method in class bunwarpj.PointToolbar
-
Mouse released.
- MOVE_CROSS - Static variable in class bunwarpj.PointAction
-
constant to identify the move cross tool
- movePoint(int, int) - Method in class bunwarpj.PointHandler
-
Move the current point into a new position.
- paint(Graphics) - Method in class bunwarpj.PointToolbar
-
Paint the buttons of the toolbar.
- Param - Class in bunwarpj
-
This class stores the parameters to apply the consistent elastic registration
and it is independent of the primary GUI.
- Param() - Constructor for class bunwarpj.Param
-
Empty constructor
- Param(int, int, int, int, double, double, double, double, double, double) - Constructor for class bunwarpj.Param
-
Full constructor
- Point(double[][], int, int, double) - Static method in class bunwarpj.MiscTools
-
Plot a point in a canvas.
- PointAction - Class in bunwarpj
-
Class for all actions related with points in the bUnwarpJ interface: moving, adding and
deleting landmarks, and painting the masks.
- PointAction(ImagePlus, PointHandler, PointToolbar, MainDialog) - Constructor for class bunwarpj.PointAction
-
Create an instance of PointAction.
- PointHandler - Class in bunwarpj
-
Class to deal with handle points in bUnwarpJ: here we have the methods
to paint the landmarks and the masks.
- PointHandler(ImagePlus, PointToolbar, Mask, MainDialog) - Constructor for class bunwarpj.PointHandler
-
Constructor with graphical capabilities, create an instance of PointHandler.
- PointHandler(ImagePlus) - Constructor for class bunwarpj.PointHandler
-
Constructor without graphical capabilities, create an instance of PointHandler.
- PointHandler(int, int) - Constructor for class bunwarpj.PointHandler
-
Constructor without graphical capabilities, create an instance of PointHandler.
- PointToolbar - Class in bunwarpj
-
Class to deal with the point toolbar option in the bUnwarpJ interface:
draw the toolbar and change between tools.
- PointToolbar(Toolbar, MainDialog) - Constructor for class bunwarpj.PointToolbar
-
Create an instance of PointToolbar.
- pop_front() - Method in class bunwarpj.CumulativeQueue
-
Pop the value from the front of the queue.
- popFromPyramid() - Method in class bunwarpj.BSplineModel
-
Pop one element from the coefficients and image pyramids.
- prec_xIndex - Variable in class bunwarpj.BSplineModel
-
precomputed x index
- prec_yIndex - Variable in class bunwarpj.BSplineModel
-
precomputed y index
- precomputed_getWeightDx(int, int, int, int) - Method in class bunwarpj.BSplineModel
-
Get precomputed weight dx.
- precomputed_getWeightDxDx(int, int, int, int) - Method in class bunwarpj.BSplineModel
-
Get precomputed weight dxdx
- precomputed_getWeightDxDy(int, int, int, int) - Method in class bunwarpj.BSplineModel
-
Get precomputed weight dxdy
- precomputed_getWeightDy(int, int, int, int) - Method in class bunwarpj.BSplineModel
-
Get precomputed weight dy
- precomputed_getWeightDyDy(int, int, int, int) - Method in class bunwarpj.BSplineModel
-
Get precomputed weight dydy
- precomputed_getWeightI(int, int, int, int) - Method in class bunwarpj.BSplineModel
-
Get precomputed weight of coefficient l,m
- precomputed_getWidth() - Method in class bunwarpj.BSplineModel
-
Get width of precomputed vectors.
- precomputed_interpolateD(double[], int, int) - Method in class bunwarpj.BSplineModel
-
Interpolate the X and Y derivatives of the image at a
given point.
- precomputed_interpolateD2(double[], int, int) - Method in class bunwarpj.BSplineModel
-
Interpolate the XY, XX and YY derivatives of the image at a
given point.
- precomputed_interpolateI(int, int) - Method in class bunwarpj.BSplineModel
-
Interpolate the image (or deformation) at a given point using
the precomputed weights.
- precomputed_prepareForInterpolation(int, int, int) - Method in class bunwarpj.BSplineModel
-
Prepare precomputations for a given image size.
- prepareForInterpolation(double, double, boolean) - Method in class bunwarpj.BSplineModel
-
If fromCurrent is true, the interpolation is prepared to be done
from the current image in the pyramid.
- prepareForInterpolationAndInterpolateI(double, double, boolean, boolean) - Method in class bunwarpj.BSplineModel
-
Prepare for interpolation and interpolate
fromSub = true: The interpolation is done from the subsampled version
of the image
- prepareForInterpolationAndInterpolateIAndD(double, double, double[], boolean, boolean) - Method in class bunwarpj.BSplineModel
-
Prepare for interpolation and interpolate the image value and its
derivatives
fromSub = true: The interpolation is done from the subsampled version
of the image
- printMatrix(String, double[][]) - Static method in class bunwarpj.MiscTools
-
Print a matrix in the command line.
- ProgressBar - Class in bunwarpj
-
This class implements the interactions when dealing with ImageJ's
progress bar.
- ProgressBar() - Constructor for class bunwarpj.ProgressBar
-
- push_back(double) - Method in class bunwarpj.CumulativeQueue
-
Push a value at the end of the queue.
- rawTransformImageMacro(String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Method to transform the source image given an raw deformation.
- rawWarpingIndex(ImagePlus, ImagePlus, int, double[][], double[][], double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Warping index for comparing elastic deformations with any kind
of deformation (both transformations having same direction).
- rawWarpingIndex(ImagePlus, ImagePlus, double[][], double[][], double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Warping index for comparing two raw deformations (both
transformations having same direction).
- rawWarpingIndex(String, String, ImagePlus, ImagePlus) - Static method in class bunwarpj.MiscTools
-
Calculate warping index between two raw transforms loaded from file.
- readFile(String) - Method in class bunwarpj.Mask
-
Read mask from file.
- record(String, String...) - Static method in class bunwarpj.IODialog
-
Macro-record a specific command.
- reduceCoeffsBy2(double[], int, int) - Method in class bunwarpj.BSplineModel
-
Reduce coefficients by a factor of 2 (beta)
- regularizeMatrix(AffineTransform, double, double) - Method in class bunwarpj.Transformation
-
Regularize matrix to remove sharing, scaling, etc.
- REMOVE_CROSS - Static variable in class bunwarpj.PointAction
-
constant to identify the remove cross tool
- removePoint() - Method in class bunwarpj.PointHandler
-
Remove the current point.
- removePoint(int) - Method in class bunwarpj.PointHandler
-
Remove one specific point.
- removePoints() - Method in class bunwarpj.PointHandler
-
Remove all points in the mask.
- repaintToolbar() - Method in class bunwarpj.MainDialog
-
Repaint toolbar.
- resampling(double[], int, int, double, int, int) - Static method in class math.BSpline
-
Geometric transform and resampling
- resetProgressBar() - Static method in class bunwarpj.ProgressBar
-
Erase the progress bar and cancel pending operations.
- resize1D(double[], int, int, int, double, boolean) - Static method in class math.BSpline
-
Ref: A.
- restoreAll() - Method in class bunwarpj.MainDialog
-
Restore the initial conditions.
- restorePreviousToolbar() - Method in class bunwarpj.PointToolbar
-
Restore the previous toolbar.
- run() - Method in class bunwarpj.BSplineModel
-
Start the image pre-computations.
- run(String) - Method in class bunwarpj.bUnwarpJ_
-
Method to lunch the plugin.
- run(String) - Method in class bunwarpj.Credits
-
Launch the credits plugin
- run() - Method in class bunwarpj.FinalAction
-
Perform the registration
- SAVE_LANDMARKS - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to save landmarks to a file
- saveDirectTransformation() - Method in class bunwarpj.Transformation
-
Save source transformation.
- saveDirectTransformation(String) - Method in class bunwarpj.Transformation
-
Save target to source transformation into a file.
- saveElasticAsRaw(String, String, ImagePlus) - Static method in class bunwarpj.MiscTools
-
Save elastic transform as raw transform.
- saveElasticTransformation(int, double[][], double[][], String) - Static method in class bunwarpj.MiscTools
-
Save the elastic transformation.
- saveInverseTransformation() - Method in class bunwarpj.Transformation
-
Save target transformation.
- saveInverseTransformation(String) - Method in class bunwarpj.Transformation
-
Save source to target transformation into a file.
- saveLandmarks(String) - Static method in class bunwarpj.bUnwarpJ_
-
Save landmarks to file.
- saveLandmarks(String, Vector<Point>, Vector<Point>) - Static method in class bunwarpj.MiscTools
-
Save source and target landmarks to file
- saveRawAsElastic(String, String, int, ImagePlus) - Static method in class bunwarpj.MiscTools
-
Save raw transform as elastic.
- saveRawTransformation(String, int, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Save a raw transformation
- scale(ImageProcessor, float) - Static method in class bunwarpj.MiscTools
-
Scale an image with good quality in both up and down direction
- setAllUp() - Method in class bunwarpj.PointToolbar
-
Enable the tool buttons.
- setAnisotropyCorrection(double) - Method in class bunwarpj.Param
-
- setAnisotropyCorrection(double) - Method in class bunwarpj.Transformation
-
Correct anisotropy on initial affine transform
- setClearMask(boolean) - Method in class bunwarpj.MainDialog
-
Set the clearMask flag.
- setCoefficients(double[], int, int, int) - Method in class bunwarpj.BSplineModel
-
Set spline coefficients.
- setCurrentPoint(int) - Method in class bunwarpj.PointHandler
-
Set the current point.
- setFinalActionLaunched(boolean) - Method in class bunwarpj.MainDialog
-
Set final action launched flag.
- setMaskPoints(Vector<Point>) - Method in class bunwarpj.Mask
-
Set the mask points.
- setPyramidDepth(int) - Method in class bunwarpj.BSplineModel
-
Sets the depth up to which the pyramids should be computed.
- setSaveTransformation(boolean) - Method in class bunwarpj.MainDialog
-
Set saveTransformation flag.
- setScaleCorrection(double) - Method in class bunwarpj.Param
-
- setScaleCorrection(double) - Method in class bunwarpj.Transformation
-
Correct scale on initial affine transform
- setSecondaryPointHandler(ImagePlus, PointHandler) - Method in class bunwarpj.PointAction
-
Set the secondary point handler.
- setSecondaryPointHandler(ImagePlus, PointHandler) - Method in class bunwarpj.PointHandler
-
Set the secondary point handler.
- setShearCorrection(double) - Method in class bunwarpj.Param
-
- setShearCorrection(double) - Method in class bunwarpj.Transformation
-
Correct shear on initial affine transform
- setSource(ImagePlus, PointHandler) - Method in class bunwarpj.PointToolbar
-
Set the source image.
- setSourceAffineMatrix(double[][]) - Method in class bunwarpj.MainDialog
-
Set source intial affine matrix.
- setSourceMask(String) - Method in class bunwarpj.MainDialog
-
Set source Mask.
- setStopRegistration() - Method in class bunwarpj.MainDialog
-
Set the stopRegistration flag to true.
- setSubsamplingFactor(int) - Method in class bunwarpj.BSplineModel
-
Set maximum sub-sampling factor
- setTarget(ImagePlus, PointHandler) - Method in class bunwarpj.PointToolbar
-
Set the target image.
- setTestSourceSet(int) - Method in class bunwarpj.PointHandler
-
Set the set of test for the source.
- setTestTargetSet(int) - Method in class bunwarpj.PointHandler
-
Set the set of test for the target.
- setTool(int) - Method in class bunwarpj.PointToolbar
-
Set the tool.
- setToolbarAllUp() - Method in class bunwarpj.MainDialog
-
Set toolbar tools all up.
- setup(ImagePlus, ImagePlus, BSplineModel, BSplineModel, PointHandler, PointHandler, Mask, Mask, double[][], double[][], int, int, int, double, double, double, double, double, double, int, boolean, int) - Method in class bunwarpj.FinalAction
-
Pass parameter from MainDialog to
FinalAction.
- setValue(int, int, boolean) - Method in class bunwarpj.Mask
-
Sets the value of the mask at a certain pixel.
- SHOW_LANDMARKS - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to show landmarks on a table
- showDialog() - Method in class bunwarpj.MainDialog
-
Show main bUnwarpJ dialog
- showDialog() - Method in class bunwarpj.Param
-
Show modal dialog to collect bUnwarpJ parameters
- showDirectResults() - Method in class bunwarpj.Transformation
-
Show the direct transformation results(multi-thread version).
- showImage(String, double[], int, int) - Static method in class bunwarpj.MiscTools
-
Show an image in a new bUnwarpJ window.
- showImage(String, double[][]) - Static method in class bunwarpj.MiscTools
-
Show an image in a new bUnwarpJ window.
- showInverseResults() - Method in class bunwarpj.Transformation
-
Show the inverse transformation results (multi-thread version).
- showLandmarks() - Static method in class bunwarpj.bUnwarpJ_
-
Show landmark points in a results window.
- showMask() - Method in class bunwarpj.Mask
-
Show mask.
- showMatrix(int, int, double[][]) - Static method in class bunwarpj.MathTools
-
Method to display the matrix in the command line.
- showPoints(Vector<Point>, Vector<Point>) - Static method in class bunwarpj.MiscTools
-
Display landmark points in a separate table
- singularValueBackSubstitution(double[][], double[], double[][], double[], double[]) - Static method in class bunwarpj.MathTools
-
solve (U.W.Transpose(V)).X == B in terms of X
{U, W, V} are given by SingularValueDecomposition
by convention, set w[i,j]=0 to get (1/w[i,j])=0
the size of the input matrix U is (Lines x Columns)
the size of the vector (1/W) of singular values is (Columns)
the size of the untransposed orthogonal matrix V is (Columns x Columns)
the size of the input vector B is (Lines)
the size of the output vector X is (Columns)
- singularValueDecomposition(double[][], double[], double[][]) - Static method in class bunwarpj.MathTools
-
Singular Value Decomposition.
- skipProgressBar(int) - Static method in class bunwarpj.ProgressBar
-
Perform stride operations at once.
- sMaxScaleDeformationChoices - Static variable in class bunwarpj.MainDialog
-
final deformation options
- sMaxScaleDeformationChoices - Variable in class bunwarpj.Param
-
maximum scale deformation choices
- sMinScaleDeformationChoices - Static variable in class bunwarpj.MainDialog
-
initial deformation options
- sMinScaleDeformationChoices - Variable in class bunwarpj.Param
-
minimum scale deformation choices
- smoothForScale(ImageProcessor, float, float, float) - Static method in class bunwarpj.MiscTools
-
Smooth with a Gaussian kernel that represents downsampling at a given
scale factor and sourceSigma.
- sRegistrationModes - Variable in class bunwarpj.Param
-
available registration modes
- startPyramids() - Method in class bunwarpj.BSplineModel
-
Start coefficient and image pyramids
- stepProgressBar() - Static method in class bunwarpj.ProgressBar
-
Perform 1 operation unit.
- STOP - Static variable in class bunwarpj.PointAction
-
constant to identify the stop tool
- stopThreshold - Variable in class bunwarpj.Param
-
stopping threshold