- c - Variable in class math3d.Triangle
-
- c - Variable in class util.Arrow
-
- calculate(String, ImagePlus, ImagePlus) - Method in class util.ImageCalculatorRevised
-
- calculateBadness(FastMatrix) - Method in class vib.RegistrationOptimizer
-
- calculateCircumcenter() - Method in class math3d.Tetrahedron
-
- calculateCircumcenter2() - Method in class math3d.Triangle
-
- calculateGrad(ImagePlus, boolean) - Static method in class process3d.Gradient
-
- calculateResult(String, ImagePlus, ImagePlus) - Method in class util.ImageCalculatorRevised
-
- callback - Variable in class features.ComputeCurvatures
-
- caller - Variable in class inference.BEPBInference
-
- caller - Variable in class inference.Inference
-
- cancel() - Method in class stacks.ThreePaneCrop
-
- cancel() - Method in class util.FindConnectedRegions
-
- cancelGaussianGeneration() - Method in class features.ComputeCurvatures
-
- CANCELLED - Static variable in interface landmarks.FineTuneProgressListener
-
- CandidateAffine(NamedPointSet, NamedPointSet, double) - Constructor for class landmarks.AffineFromLandmarks.CandidateAffine
-
- center - Variable in class math3d.Triangle
-
- CENTER - Static variable in class vib.app.Options
-
- CenterTransformation - Class in vib.app.module
-
- CenterTransformation() - Constructor for class vib.app.module.CenterTransformation
-
- centerX - Variable in class vib.app.ImageMetaData.Material
-
- centerX(int) - Method in class vib.app.module.TissueStatistics.Statistics
-
- centerY - Variable in class vib.app.ImageMetaData.Material
-
- centerY(int) - Method in class vib.app.module.TissueStatistics.Statistics
-
- centerZ - Variable in class vib.app.ImageMetaData.Material
-
- centerZ(int) - Method in class vib.app.module.TissueStatistics.Statistics
-
- changeLabelfieldToGray() - Method in class amira.AmiraParameters
-
- channels - Variable in class util.BatchOpener.ChannelsAndLoader
-
- ChannelsAndLoader(ImagePlus[], String) - Constructor for class util.BatchOpener.ChannelsAndLoader
-
- CHECKBOX - Static variable in class util.ModelessQuestions
-
- checkMemory(ImagePlus, int) - Method in class stacks.ThreePanes
-
- CIELAB - Class in color
-
- CIELAB() - Constructor for class color.CIELAB
-
- CIELAB2sRGB(float[], float[]) - Static method in class color.CIELAB
-
- CIELAB2XYZ(float[], float[]) - Static method in class color.CIELAB
-
- CircleIterators - Class in vib.edge
-
- CircleIterators() - Constructor for class vib.edge.CircleIterators
-
- circumcenter(Pnt[]) - Static method in class delaunay.Pnt
-
Circumcenter of a simplex.
- clamp(int) - Method in class vib.segment.CustomStackWindow
-
- classify() - Method in class process3d.FindMinima
-
- classifyPixel(int, int, int) - Method in class process3d.FindMinima
-
- clean(Roi, byte[], int, byte) - Static method in class oldsegmenters.LabelBinaryOps
-
- cleanUp() - Method in class vib.segment.CustomStackWindow
-
- clear() - Method in class vib.app.gui.Console
-
- clear() - Method in class vib.PointList
-
- client - package client
-
- clone() - Method in class features.ComputeCurvatures.FloatArray
-
- clone() - Method in class features.ComputeCurvatures.FloatArray2D
-
- clone() - Method in class features.ComputeCurvatures.FloatArray3D
-
- clone(double[][]) - Static method in class math3d.FastMatrixN
-
- clone(float[][]) - Static method in class math3d.FloatMatrixN
-
- clone() - Method in class vib.app.FileGroup
-
- clone() - Method in class vib.app.Options
-
- clone() - Method in class vib.segment.Border
-
Returns a clone of this Border
- clone() - Method in class vib.transforms.OrderedTransformations
-
- cloneDimensionsOnly() - Method in class vib.InterpolatedImage
-
- cloneDimensionsOnly(ImagePlus, int) - Static method in class vib.InterpolatedImage
-
- cloneImage() - Method in class vib.InterpolatedImage
-
- close(ImageProcessor, Roi, byte) - Static method in class oldsegmenters.LabelBinaryOps
-
- close() - Method in class util.ModelessQuestions
-
- close() - Method in class util.opencsv.CSVReader
-
Closes the underlying reader.
- close() - Method in class util.opencsv.CSVWriter
-
Close the underlying stream writer flushing any buffered content.
- closeAllWithoutConfirmation() - Static method in class util.WindowHelpers
-
- closeAndReset() - Method in class stacks.ThreePaneContainer
-
- closeAndReset() - Method in class stacks.ThreePanes
-
- closeChannelsWithTag(String) - Method in class client.ArchiveClient
-
- CMTKTransformation - Class in util
-
- CMTKTransformation() - Constructor for class util.CMTKTransformation
-
- CMTKTransformation(int, int, int, double, double, double, double, double, double, double[][]) - Constructor for class util.CMTKTransformation
-
- CMTKTransformation.Inverse - Class in util
-
- color - package color
-
- colors - Variable in class amira.AmiraParameters.Material
-
- CombinationGenerator - Class in util
-
- CombinationGenerator(int, int) - Constructor for class util.CombinationGenerator
-
- compareTo(Object) - Method in class landmarks.RegistrationResult
-
- compareTo(Object) - Method in class oldsegmenters.AutoLabeller.LabelStats
-
- compareTo(FindConnectedRegions.Region) - Method in class util.FindConnectedRegions.Region
-
- COMPLETED - Static variable in interface landmarks.FineTuneProgressListener
-
- composeWith(FastMatrix) - Method in class vib.FastMatrix
-
- composeWith(FloatMatrix) - Method in class vib.FloatMatrix
-
- composeWith(Transform) - Method in class vib.transforms.BooksteinTransform
-
- composeWith(Transform) - Method in class vib.transforms.FastMatrixTransform
-
- composeWith(Transform) - Method in interface vib.transforms.Transform
-
- composeWithFastMatrix(FastMatrix) - Method in class vib.transforms.FastMatrixTransform
-
- ComputeCurvatures - Class in features
-
Principle Curvature Plugin for ImageJ
- ComputeCurvatures() - Constructor for class features.ComputeCurvatures
-
- ComputeCurvatures(ImagePlus, double, GaussianGenerationCallback, boolean) - Constructor for class features.ComputeCurvatures
-
- ComputeCurvatures.FloatArray - Class in features
-
This class is the abstract class for my FloatArrayXDs,
which are a one dimensional structures with methods for access in n dimensions
- ComputeCurvatures.FloatArray2D - Class in features
-
The 2D implementation of the FloatArray
- ComputeCurvatures.FloatArray3D - Class in features
-
The 3D implementation of the FloatArray
- computeEigenValues(double[][]) - Method in class features.ComputeCurvatures
-
This method computes the Eigenvalues of the Hessian Matrix, the
Eigenvalues correspond to the Principle Curvatures.
- computeEigenValues(float[][]) - Method in class features.ComputeCurvatures
-
This method computes the Eigenvalues of the Hessian Matrix, the
Eigenvalues correspond to the Principle Curvatures.
- computeGaussianFastMirror(ComputeCurvatures.FloatArray2D, float, GaussianGenerationCallback, Calibration) - Method in class features.ComputeCurvatures
-
This method does the gaussian filtering of an image.
- computeGaussianFastMirror(ComputeCurvatures.FloatArray3D, float, GaussianGenerationCallback, Calibration) - Method in class features.ComputeCurvatures
-
This method does the gaussian filtering of an 3D image.
- computeHessianMatrix2DDouble(ComputeCurvatures.FloatArray2D, int, int, double, float, float) - Method in class features.ComputeCurvatures
-
This method computes the Hessian Matrix for the 3x3 environment of a certain pixel
The 3D Hessian Matrix:
xx xy
yx yy
- computeHessianMatrix2DFloat(ComputeCurvatures.FloatArray2D, int, int, double, float, float) - Method in class features.ComputeCurvatures
-
This method computes the Hessian Matrix for the 3x3 environment of a certain pixel
The 3D Hessian Matrix:
xx xy
yx yy
- computeHessianMatrix3DDouble(ComputeCurvatures.FloatArray3D, int, int, int, double, float, float, float) - Method in class features.ComputeCurvatures
-
This method computes the Hessian Matrix for the 3x3x3 environment of a certain voxel
The 3D Hessian Matrix:
xx xy xz
yx yy yz
zx zy zz
- computeHessianMatrix3DFloat(ComputeCurvatures.FloatArray3D, int, int, int, double, float, float, float) - Method in class features.ComputeCurvatures
-
This method computes the Hessian Matrix for the 3x3x3 environment of a certain voxel
The 3D Hessian Matrix:
xx xy xz
yx yy yz
zx zy zz
- CONFIG_FILE - Static variable in class vib.app.Options
-
- Connectivity2D - Class in adt
-
a structure that partitions points added into it into connected islands (of Points)
Probably could do with a speedup...
- Connectivity2D() - Constructor for class adt.Connectivity2D
-
- Console - Class in vib.app.gui
-
- console - Variable in class vib.app.module.Module
-
- contains(Point) - Method in class adt.Points
-
- contains(Simplex) - Method in class delaunay.Triangulation
-
True iff the simplex is in this Triangulation.
- content(Pnt[]) - Static method in class delaunay.Pnt
-
Determine the signed content (i.e., area or volume, etc.) of a simplex.
- convertToLuminance(ImagePlus) - Static method in class util.RGBToLuminance
-
Takes an RGB ImagePlus and converts it to a 8-bit grey
ImagePlus of luminance values.
- convolve(ImagePlus, float[], float[], float[]) - Static method in class process3d.Convolve3d
-
- convolve(ImagePlus, float[][][]) - Static method in class process3d.Convolve3d
-
- convolve(ImagePlus, int) - Static method in class process3d.MinMaxMedian
-
Main method which iterates through the stack and calls
convolvePoint() for each voxel.
- Convolve3d - Class in process3d
-
- Convolve3d() - Constructor for class process3d.Convolve3d
-
- convolveX(ImagePlus, float[]) - Static method in class process3d.Convolve3d
-
- convolveY(ImagePlus, float[]) - Static method in class process3d.Convolve3d
-
- convolveZ(ImagePlus, float[]) - Static method in class process3d.Convolve3d
-
- coord(int) - Method in class delaunay.Pnt
-
- coordinatesAsString() - Method in class vib.BenesNamedPoint
-
- copy(FileGroup) - Method in class vib.app.FileGroup
-
- copy(Options) - Method in class vib.app.Options
-
- copy - Variable in class vib.segment.Thresholder
-
- copy - Variable in class vib.ShowHistogram
-
- copyFrom(FloatMatrix) - Method in class vib.FastMatrix
-
- copyFrom(FloatMatrix) - Method in class vib.FloatMatrix
-
- copyIntoPalette(ImagePlus, ImagePlus, int, int) - Method in class features.SigmaPalette
-
- copyToClipboard() - Method in class vib.ShowHistogram
-
- copyToFlatDoubleArray(double[]) - Method in class vib.FastMatrix
-
- copyToFlatFloatArray(float[]) - Method in class vib.FloatMatrix
-
- correctChannel(ImagePlus) - Method in class util.FileAndChannel
-
- correctFileName(ImagePlus) - Method in class util.FileAndChannel
-
- Correlation - Class in distance
-
- Correlation() - Constructor for class distance.Correlation
-
- correlation() - Method in class distance.Correlation
-
- CORRELATION - Static variable in class landmarks.NamePoints
-
- count - Variable in class inference.BEPBInference
-
- count - Variable in class inference.Inference
-
- count - Variable in class inference.MAPInference
-
- count - Variable in class vib.app.ImageMetaData.Material
-
- count - Variable in class vib.app.module.TissueStatistics.Statistics
-
- count - Variable in class vib.ShowHistogram
-
- cRadius2 - Variable in class math3d.Triangle
-
- createCanvas(ImagePlus, int) - Method in class stacks.ThreePaneContainer
-
- createCanvas(ImagePlus, int) - Method in class stacks.ThreePaneCrop
-
- createCanvas(ImagePlus, int) - Method in class stacks.ThreePanes
-
- createContoursIfNotExist(int) - Method in class vib.SegmentationViewerCanvas
-
- createField(String, String, ActionListener) - Static method in class gui.GuiBuilder
-
- createGaussianKernel(float, float) - Static method in class process3d.Smooth
-
- createGaussianKernel1D(float, boolean) - Static method in class features.ComputeCurvatures
-
This method creates a gaussian kernel
- createKernel(float, float, boolean) - Static method in class process3d.Smooth
-
- createNewImage(ImagePlus, ImagePlus, boolean) - Method in class vib.transforms.OrderedTransformations
-
- createNewImageReal(ImagePlus, ImagePlus, int, int, int, int, int, int, boolean) - Method in class vib.transforms.OrderedTransformations
-
- createNewImageSingle(ImagePlus, int, int, int, int, int, int) - Method in class vib.transforms.OrderedTransformations
-
- createNewImageSingle(ImagePlus, ImagePlus, boolean) - Method in class vib.transforms.OrderedTransformations
-
- createOverlay() - Method in class process3d.FindMinima
-
- createPopup() - Method in class vib.segment.MaterialList
-
- createUniformKernel(float, float) - Static method in class process3d.Smooth
-
- cross(Pnt[]) - Static method in class delaunay.Pnt
-
Compute generalized cross-product of the rows of a matrix.
- crossProduct(double[], double[]) - Static method in class vib.FastMatrix
-
- crossProduct(float[], float[]) - Static method in class vib.FloatMatrix
-
- CSVReader - Class in util.opencsv
-
A very simple CSV reader released under a commercial-friendly license.
- CSVReader(Reader) - Constructor for class util.opencsv.CSVReader
-
Constructs CSVReader using a comma for the separator.
- CSVReader(Reader, char) - Constructor for class util.opencsv.CSVReader
-
Constructs CSVReader with supplied separator.
- CSVReader(Reader, char, char) - Constructor for class util.opencsv.CSVReader
-
Constructs CSVReader with supplied separator and quote char.
- CSVReader(Reader, char, char, int) - Constructor for class util.opencsv.CSVReader
-
Constructs CSVReader with supplied separator and quote char.
- CSVWriter - Class in util.opencsv
-
A very simple CSV writer released under a commercial-friendly license.
- CSVWriter(Writer) - Constructor for class util.opencsv.CSVWriter
-
Constructs CSVWriter using a comma for the separator.
- CSVWriter(Writer, char) - Constructor for class util.opencsv.CSVWriter
-
Constructs CSVWriter with supplied separator.
- CSVWriter(Writer, char, char) - Constructor for class util.opencsv.CSVWriter
-
Constructs CSVWriter with supplied separator and quote char.
- CSVWriter(Writer, char, char, char) - Constructor for class util.opencsv.CSVWriter
-
Constructs CSVWriter with supplied separator and quote char.
- CSVWriter(Writer, char, char, String) - Constructor for class util.opencsv.CSVWriter
-
Constructs CSVWriter with supplied separator and quote char.
- CSVWriter(Writer, char, char, char, String) - Constructor for class util.opencsv.CSVWriter
-
Constructs CSVWriter with supplied separator, quote char, escape char and line ending.
- CURRENT_MATERIAL - Static variable in class oldsegmenters.SegmentatorModel
-
- currentMaterialColor() - Method in class vib.segment.MaterialList
-
- currentMaterialID() - Method in class vib.segment.MaterialList
-
- currentMaterialID() - Method in class vib.segment.Sidebar
-
- curx - Variable in class inference.BinClassificationInference
-
- CustomCanvas - Class in vib.segment
-
- CustomCanvas(ImagePlus) - Constructor for class vib.segment.CustomCanvas
-
- CustomCanvas.CanvasListener - Interface in vib.segment
-
- CustomStackWindow - Class in vib.segment
-
- CustomStackWindow(ImagePlus) - Constructor for class vib.segment.CustomStackWindow
-
- cX - Variable in class vib.app.module.TissueStatistics.Statistics
-
- cY - Variable in class vib.app.module.TissueStatistics.Statistics
-
- cZ - Variable in class vib.app.module.TissueStatistics.Statistics
-
- gamma2linear(float) - Static method in class color.CIELAB
-
- gauss(float, float) - Static method in class process3d.Smooth
-
- GaussianGenerationCallback - Interface in features
-
- generateAffine(NamedPointWorld, NamedPointWorld, NamedPointWorld, NamedPointWorld, NamedPointWorld, NamedPointWorld, NamedPointWorld, NamedPointWorld) - Static method in class landmarks.AffineFromLandmarks
-
- generateImage(ImagePlus) - Method in class features.HessianEvalueProcessor
-
- generateTransformation() - Method in class landmarks.BooksteinFromLandmarks
-
- generateTransformation(NamedPointSet, NamedPointSet) - Method in class landmarks.BooksteinFromLandmarks
-
- generateTransformation() - Method in class vib.oldregistration.RegistrationAlgorithm
-
- get(int, int, int) - Method in interface adt.Byte3DArray
-
- get(int, int, int) - Method in class adt.Sparse3DByteArray
-
- get(int, int, int) - Method in class adt.Unsparse3DByteArray
-
- get(String) - Method in class amira.AmiraParameters
-
- get(String) - Method in class amira.AmiraTable
-
- get(int, int) - Method in class features.ComputeCurvatures.FloatArray2D
-
- get(int, int, int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- get(int) - Method in class landmarks.NamedPointSet
-
- get(String) - Method in class landmarks.NamedPointSet
-
- get(boolean) - Method in class landmarks.NamePoints
-
- get(long) - Method in class util.FindConnectedRegions.PointState
-
- get(double, double, double) - Method in interface vib.InterpolatedImage.Interpolate
-
- get(double, double, double) - Method in class vib.InterpolatedImage.NearestNeighbourByte
-
- get(int[][]) - Method in class vib.MaxEntHistogram
-
- get() - Method in class vib.NaiveResampler.Averager
-
- get() - Method in class vib.NaiveResampler.IntAverager
-
- get() - Method in class vib.NaiveResampler.MaxLikelihood
-
- get() - Method in class vib.NaiveResampler.MinEntropy
-
- get(int) - Method in class vib.PointList
-
- get(String) - Method in class vib.PointList
-
- getActionCommand() - Method in class vib.segment.ImageButton
-
- getArmedBorder() - Method in class vib.segment.ImageButton
-
Gets the border to display when the button is pressed and the mouse
is still over the button.
- getArmedImage() - Method in class vib.segment.ImageButton
-
Gets the image to display when the button is pressed and the mouse
is still over the button.
- getBaseName(int) - Method in class vib.app.module.State
-
- getBaseName(String) - Static method in class vib.app.module.State
-
- getBorder() - Method in class vib.segment.Border
-
Returns the current border color.
- getBorderThickness() - Method in class vib.segment.Border
-
Returns the current setting for the border thickness
- getBottomMargin() - Method in class vib.segment.Border
-
Returns the bottom margin.
- getBoundary(int) - Method in class inference.BEPBBinBoundariesInference
-
- getBoundary(int) - Method in class inference.BinBoundariesComputation
-
- getBoundary(int) - Method in class inference.BinBoundariesInference
-
- getBoundary(int) - Method in class inference.MAPInference
-
- getButtonState() - Method in class vib.segment.ImageButton
-
Gets the current buttonState id for the button
- getChannelName(int) - Method in class vib.app.module.State
-
- getChannelZeroIndexed() - Method in class util.FileAndChannel
-
- getColorModel() - Method in class amira.AmiraParameters
-
- getColumn(double[][], int) - Static method in class math3d.JacobiDouble
-
- getColumn(float[][], int) - Static method in class math3d.JacobiFloat
-
- getCommentStrings() - Method in class nrrd.NrrdHeader
-
- getCompletingButtonIndex() - Method in class util.ModelessQuestions
-
- getComponentTransform(int) - Method in class vib.transforms.OrderedTransformations
-
- getCount(int, int) - Method in class inference.BEPBInference
-
- getCount(int, int) - Method in class inference.Inference
-
- getCount(int, int) - Method in class inference.MAPInference
-
- getCurrentMaterial() - Method in class oldsegmenters.SegmentatorModel
-
- getCustomCanvas() - Method in class vib.segment.CustomStackWindow
-
- getCustomStackWindow() - Method in class vib.segment.SegmentationEditor
-
- getDefaultMaterialID() - Method in class vib.segment.MaterialList
-
- getDepth() - Method in class vib.InterpolatedImage
-
- getDifferenceImage() - Method in class vib.TransformedImage
-
- getDir() - Method in class video.VideoStack
-
- getDisabledBorder() - Method in class vib.segment.ImageButton
-
Gets the border to display when the button is disabled.
- getDisabledImage() - Method in class vib.segment.ImageButton
-
Gets the image to display when the button is disabled.
- getDisplacementField() - Method in class vib.DiffusionInterpol2
-
- getDistance() - Method in class vib.TransformedImage
-
- getDistances() - Method in class process3d.DistanceTransform3D
-
- getDomain() - Method in class vib.oldregistration.RegistrationAlgorithm
-
- getDouble(int, int, int) - Method in interface adt.Byte3DArray
-
- getDouble(int, int, int) - Method in class adt.Sparse3DByteArray
-
returns a scaled double between 0 and 1
- getDouble(int, int, int) - Method in class adt.Unsparse3DByteArray
-
- getDoubleField(String) - Method in class nrrd.NrrdInfo
-
- getDoubleFieldChecked(String, int, boolean) - Method in class nrrd.NrrdInfo
-
- getEigenMatrix() - Method in class math3d.JacobiDouble
-
- getEigenMatrix() - Method in class math3d.JacobiFloat
-
- getEigenValues() - Method in class math3d.JacobiDouble
-
returns the eigenvalues corresponding to
the eigenvectors
- getEigenValues() - Method in class math3d.JacobiFloat
-
returns the eigenvalues corresponding to
the eigenvectors
- getEigenVectors() - Method in class math3d.JacobiDouble
-
returns the eigenvectors as an array,
such that result[0] is the first vector
- getEigenVectors() - Method in class math3d.JacobiFloat
-
returns the eigenvectors as an array,
such that result[0] is the first vector
- getEntropy1() - Method in class distance.MutualInformation
-
- getEntropy2() - Method in class distance.MutualInformation
-
- getEulerMatrix(double[]) - Static method in class vib.RegistrationOptimizer
-
- getEulerMatrix(double, double, double, double, double, double, double, double, double) - Static method in class vib.RegistrationOptimizer
-
- getEvalues(double[]) - Method in class math3d.Eigensystem2x2Double
-
- getEvalues() - Method in class math3d.Eigensystem2x2Double
-
- getEvalues(float[]) - Method in class math3d.Eigensystem2x2Float
-
- getEvalues() - Method in class math3d.Eigensystem2x2Float
-
- getEvalues(double[]) - Method in class math3d.Eigensystem3x3Double
-
- getEvalues() - Method in class math3d.Eigensystem3x3Double
-
- getEvalues(float[]) - Method in class math3d.Eigensystem3x3Float
-
- getEvalues() - Method in class math3d.Eigensystem3x3Float
-
- getEvaluesCopy() - Method in class math3d.Eigensystem2x2Double
-
- getEvaluesCopy() - Method in class math3d.Eigensystem2x2Float
-
- getEvaluesCopy() - Method in class math3d.Eigensystem3x3Double
-
- getEvaluesCopy() - Method in class math3d.Eigensystem3x3Float
-
- getFieldStrings() - Method in class nrrd.NrrdHeader
-
- getFileInfo(String, String) - Method in class leica.LeicaSPReader
-
- getFloating() - Method in class vib.oldregistration.RegistrationAlgorithm
-
- getHeight() - Method in class vib.InterpolatedImage
-
- getHeight() - Method in class video.VideoStack
-
- getHistogram() - Method in class vib.ShowHistogram
-
- getImage(int) - Method in class leica.LeicaSPReader
-
- getImage(String) - Method in class vib.app.module.State
-
- getImage() - Method in class vib.InterpolatedImage
-
- getImage() - Method in class vib.segment.CustomCanvas
-
- getImageCount() - Method in class vib.app.module.State
-
- getImagePath(int, int) - Method in class vib.app.module.State
-
- getIndex(String) - Method in class vib.app.FileGroup
-
- getIndexOf(String) - Method in class vib.segment.MaterialList
-
- getIndexOfPoint(String) - Method in class landmarks.NamedPointSet
-
- getInitialCenters() - Method in class vib.RegistrationOptimizer
-
- getInsets() - Method in class vib.segment.Border
-
returns the left, right, top, and bottom insets of the background of the
current style, taking into account thickness and margins.
- getInt(double, double, double) - Method in class vib.InterpolatedImage.NearestNeighbourByte
-
- getIntegerField(String) - Method in class nrrd.NrrdInfo
-
- getIntegerFieldChecked(String, int, boolean) - Method in class nrrd.NrrdInfo
-
- getIntensityProbs(byte) - Method in class oldsegmenters.AutoLabeller
-
returns(normailized) probs of a label given its intensity (label id given my amterialIds)
- getIslands() - Method in class adt.Connectivity2D
-
- getItem(int) - Method in class vib.segment.MaterialList
-
- getItemCount() - Method in class vib.segment.MaterialList
-
- getJointEntropy() - Method in class distance.MutualInformation
-
- getLabelCanvas() - Method in class oldsegmenters.SegmentatorModel
-
- getLabelImagePlus() - Method in class oldsegmenters.SegmentatorModel
-
- getLabels() - Method in class vib.segment.CustomStackWindow
-
- getLabels() - Method in class vib.segment.SegmentationEditor
-
- getLabels() - Method in class vib.SegmentationViewerCanvas
-
- getLastResult() - Static method in class vib.RigidRegistration
-
- getLeftMargin() - Method in class vib.segment.Border
-
Returns the left margin.
- getLongField(String) - Method in class nrrd.NrrdInfo
-
- getLongFieldChecked(String, int, boolean) - Method in class nrrd.NrrdInfo
-
- getLowerBound(int) - Method in class landmarks.AffineFromLandmarks.CandidateAffine
-
- getLowerBound(int) - Method in class landmarks.TransformationAttempt
-
- getMapping(boolean) - Method in class vib.MaxEntHistogram
-
after quantization, returns a mapping from old pixel values
to new pixel values.
- getMaterial(int) - Method in class amira.AmiraParameters
-
- getMaterial(int) - Method in class distance.TwoValues
-
- getMaterial(String) - Method in class vib.app.ImageMetaData
-
- getMaterialColor(int) - Method in class amira.AmiraParameters
-
- getMaterialCount() - Method in class amira.AmiraParameters
-
- getMaterialID(String) - Method in class amira.AmiraParameters
-
- getMaterialIndex(String) - Method in class vib.app.ImageMetaData
-
- getMaterialList() - Method in class amira.AmiraParameters
-
- getMaterialName(int) - Method in class amira.AmiraParameters
-
- getMaterialParams() - Method in class oldsegmenters.SegmentatorModel
-
- getMaterials() - Method in class amira.AmiraParameters
-
- getMaterials() - Method in class vib.segment.Sidebar
-
- getMatrix(String) - Method in class vib.app.ImageMetaData
-
- getMax() - Method in class features.SigmaPalette
-
- getMaxProb() - Method in class inference.DistributionInference
-
- getMean() - Method in class math3d.NormalEstimator
-
- getMeanSequenceLength() - Method in class adt.PixelStats
-
- getMessage() - Method in class vib.app.module.AverageBrain
-
- getMessage() - Method in class vib.app.module.CenterTransformation
-
- getMessage() - Method in class vib.app.module.EndModule
-
- getMessage() - Method in class vib.app.module.GreyTransformation
-
- getMessage() - Method in class vib.app.module.Label
-
- getMessage() - Method in class vib.app.module.LabelCenterTransformation
-
- getMessage() - Method in class vib.app.module.LabelDiffusionTransformation
-
- getMessage() - Method in class vib.app.module.Module
-
- getMessage() - Method in class vib.app.module.Resample
-
- getMessage() - Method in class vib.app.module.ResampleLabels
-
- getMessage() - Method in class vib.app.module.Show
-
- getMessage() - Method in class vib.app.module.SplitChannels
-
- getMessage() - Method in class vib.app.module.TissueStatistics
-
- getMessage() - Method in class vib.app.module.TransformImages
-
- getMinAndMax(ImagePlus, float[]) - Static method in class process3d.Rebin
-
- getMinimumSize() - Method in class vib.segment.CustomCanvas
-
- getMinimumSize() - Method in class vib.segment.CustomStackWindow
-
- getMinProb() - Method in class inference.DistributionInference
-
- getMirror(int, int) - Method in class features.ComputeCurvatures.FloatArray2D
-
- getMirror(int, int, int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- getModel() - Method in class vib.oldregistration.RegistrationAlgorithm
-
- getN() - Method in class adt.PixelStats
-
- getName() - Method in class landmarks.NamedPointWorld
-
- getName() - Method in class vib.app.module.AverageBrain
-
- getName() - Method in class vib.app.module.CenterTransformation
-
- getName() - Method in class vib.app.module.EndModule
-
- getName() - Method in class vib.app.module.GreyTransformation
-
- getName() - Method in class vib.app.module.Label
-
- getName() - Method in class vib.app.module.LabelCenterTransformation
-
- getName() - Method in class vib.app.module.LabelDiffusionTransformation
-
- getName() - Method in class vib.app.module.Module
-
- getName() - Method in class vib.app.module.Resample
-
- getName() - Method in class vib.app.module.ResampleLabels
-
- getName() - Method in class vib.app.module.Show
-
- getName() - Method in class vib.app.module.SplitChannels
-
- getName() - Method in class vib.app.module.TissueStatistics
-
- getName() - Method in class vib.app.module.TransformImages
-
- getName() - Method in class vib.BenesNamedPoint
-
- getNamesAsSet() - Method in class landmarks.NamedPointSet
-
- getNearestByte(double, double, double) - Method in class vib.InterpolatedImage
-
- getNeighbours(Point) - Static method in class adt.Connectivity2D
-
4 nieghbours per point
- getNext() - Method in class util.CombinationGenerator
-
- getNoCheck(int, int, int) - Method in class vib.InterpolatedImage
-
- getNoCheckFloat(int, int, int) - Method in class vib.InterpolatedImage
-
- getNoCheckInt(int, int, int) - Method in class vib.InterpolatedImage
-
- getNoCheckShort(int, int, int) - Method in class vib.InterpolatedImage
-
- getNoInterpol(int, int, int) - Method in class vib.InterpolatedImage
-
- getNoInterpolFloat(int, int, int) - Method in class vib.InterpolatedImage
-
- getNoInterpolInt(int, int, int) - Method in class vib.InterpolatedImage
-
- getNoInterpolShort(int, int, int) - Method in class vib.InterpolatedImage
-
- getNormal() - Method in class math3d.NormalEstimator
-
- getNormal() - Method in class math3d.Plane
-
- getNumArguments() - Method in class landmarks.AffineFromLandmarks.CandidateAffine
-
- getNumArguments() - Method in class landmarks.TransformationAttempt
-
- getNumberOfChannels() - Method in class leica.LeicaSPReader
-
- getNumberOfPoints() - Method in class util.FindConnectedRegions.Region
-
- getNumberOfRotations() - Method in class math3d.JacobiDouble
-
returns the number of rotations needed to
converge
- getNumberOfRotations() - Method in class math3d.JacobiFloat
-
returns the number of rotations needed to
converge
- getNumLeft() - Method in class util.CombinationGenerator
-
- getOriginalImage() - Method in class oldsegmenters.SegmentatorModel
-
- getOutline() - Method in class adt.Points
-
- getOutline(int, int) - Method in class vib.SegmentationViewerCanvas
-
- getOutputPath(int) - Method in class vib.app.module.State
-
- getOverBorder() - Method in class vib.segment.ImageButton
-
Gets the border to display when the button is not pressed and the mouse
is over the button.
- getOverImage() - Method in class vib.segment.ImageButton
-
Gets the image to display when the button is not pressed and the mouse
is over the button.
- getParameters() - Method in class amira.AmiraTable
-
- getParameterString(int, String[]) - Static method in class amira.AmiraTable
-
- getPath() - Method in class util.FileAndChannel
-
- getPixelProb(byte) - Method in class oldsegmenters.AutoLabeller.LabelStats
-
- getPoint(String) - Method in class landmarks.NamedPointSet
-
- getPoint3DArrayForNames(String[]) - Method in class landmarks.NamedPointSet
-
- getPointNames() - Method in class landmarks.NamedPointSet
-
- getPoints() - Method in class adt.Points
-
- getPos(int, int) - Method in class features.ComputeCurvatures.FloatArray2D
-
- getPos(int, int, int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- getPosteriorProb() - Method in class inference.MAPInference
-
- getPreferredSize() - Method in class vib.segment.ImageButton
-
Overrides awt.Component.preferredSize() to return the preferred size of the button.
- getPreview() - Method in class video.VideoStack
-
- getPreviewHeight() - Method in class video.VideoStack
-
- getPreviewWidth() - Method in class video.VideoStack
-
- getProb(byte) - Method in class adt.PixelStats
-
prob
- getProbability(int) - Method in class inference.DistributionInference
-
- getProcessor(int) - Method in class video.VideoStack
-
- getProperties() - Method in class amira.AmiraTable
-
- getProperty(String) - Method in class amira.AmiraParameters
-
- getProperty(Hashtable, String, String) - Method in class amira.AmiraParameters
-
- getResampledPath(int, int) - Method in class vib.app.module.State
-
- getResult() - Method in class vib.app.module.TissueStatistics.Statistics
-
- getResult() - Method in class vib.FastMatrix
-
- getResult() - Method in class vib.FloatMatrix
-
- getRightMargin() - Method in class vib.segment.Border
-
Returns the right margin.
- getRoi(int) - Method in class vib.segment.CustomStackWindow
-
- getSelected() - Method in class vib.app.gui.FileGroupDialog
-
- getSelectedItem() - Method in class vib.segment.MaterialList
-
- getSelectedSigmaIndex() - Method in class features.SigmaPalette
-
- getSidebar() - Method in class vib.segment.CustomStackWindow
-
- getSize() - Method in class adt.Points
-
- getSource() - Method in class events.RoiEvent
-
- getSource() - Method in class events.SliceEvent
-
- getSpatialProbs(int, int, int) - Method in class oldsegmenters.AutoLabeller
-
returns(normailized) probs of a label given its location
- getStack() - Method in class amira.AmiraMeshDecoder
-
Get AmiraMesh data as a stack.
- getStackFast() - Method in class amira.AmiraMeshDecoder
-
Get AmiraMesh data as a stack in a fast way, at a cost of reading the
whole image information at once.
- getStackLimits(ImagePlus) - Static method in class util.Limits
-
- getStackLimits(ImagePlus, boolean) - Static method in class util.Limits
-
- getStandardType(String) - Method in class nrrd.NrrdInfo
-
- getStatistics(int) - Method in class vib.app.module.State
-
- getStatistics(ImagePlus) - Static method in class vib.app.module.TissueStatistics
-
- getStatisticsPath() - Method in class vib.app.module.State
-
- getStatisticsPath(int) - Method in class vib.app.module.State
-
- getStringField(String) - Method in class nrrd.NrrdInfo
-
- getStringFieldChecked(String, int, boolean) - Method in class nrrd.NrrdInfo
-
- getTable() - Method in class amira.AmiraMeshDecoder
-
- getTagStrings() - Method in class nrrd.NrrdHeader
-
- getTemplate() - Method in class vib.app.module.State
-
- getTemplate() - Method in class vib.oldregistration.RegistrationAlgorithm
-
- getTemplate() - Method in class vib.TransformedImage
-
- getTemplateBaseName() - Method in class vib.app.module.State
-
- getTemplateButton() - Method in class vib.app.gui.FileGroupDialog
-
- getTemplateLabels() - Method in class vib.app.module.State
-
- getTextData() - Method in class nrrd.NrrdHeader
-
- getTopMargin() - Method in class vib.segment.Border
-
Returns the top margin.
- getTotal() - Method in class math3d.NormalEstimator
-
- getTotal() - Method in class util.CombinationGenerator
-
- getTransformed(ImagePlus, int) - Method in class process3d.DistanceTransform3D
-
- getTransformed() - Method in class vib.TransformedImage
-
- getTransformLabel() - Method in class vib.app.module.State
-
- getTransformLabel(int) - Method in class vib.app.module.State
-
- getTransformMatrix(int) - Method in class vib.app.module.State
-
- getTransformType() - Method in class vib.transforms.BooksteinTransform
-
- getTransformType() - Method in class vib.transforms.FastMatrixTransform
-
- getTransformType() - Method in interface vib.transforms.Transform
-
- getType() - Method in class vib.segment.Border
-
Returns the border type (e.g., Border.LINE)
- getUnarmedBorder() - Method in class vib.segment.ImageButton
-
Gets the border to display when the button is not pressed or hilited
because of a mouse-over.
- getUnarmedImage() - Method in class vib.segment.ImageButton
-
Gets the image to display when the button is not pressed or hilited
because of a mouse-over.
- getUpperBound(int) - Method in class landmarks.AffineFromLandmarks.CandidateAffine
-
- getUpperBound(int) - Method in class landmarks.TransformationAttempt
-
- getUpperLeftNeigbours(Point) - Static method in class adt.Connectivity2D
-
2 negihbours (with lower x or y values
- getValue(String) - Method in class client.ArchiveClient
-
- getValue() - Method in class util.FindConnectedRegions.Region
-
- getValuesRange(ImagePlus) - Static method in class util.OverlayRegistered
-
- getValuesRange() - Method in class vib.TransformedImage
-
- getVarianceSequenceLength() - Method in class adt.PixelStats
-
- getWarpedPath(int, int) - Method in class vib.app.module.State
-
- getWidth() - Method in class vib.InterpolatedImage
-
- getWidth() - Method in class video.VideoStack
-
- getWindowList() - Static method in class amira.AmiraParameters
-
- getxMax() - Method in interface adt.Byte3DArray
-
- getxMax() - Method in class adt.Sparse3DByteArray
-
- getxMax() - Method in class adt.Unsparse3DByteArray
-
- getxMin() - Method in interface adt.Byte3DArray
-
- getxMin() - Method in class adt.Sparse3DByteArray
-
- getxMin() - Method in class adt.Unsparse3DByteArray
-
- getXPlane(int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- getXPlane_float(int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- getyMax() - Method in interface adt.Byte3DArray
-
- getyMax() - Method in class adt.Sparse3DByteArray
-
- getyMax() - Method in class adt.Unsparse3DByteArray
-
- getyMin() - Method in interface adt.Byte3DArray
-
- getyMin() - Method in class adt.Sparse3DByteArray
-
- getyMin() - Method in class adt.Unsparse3DByteArray
-
- getYPlane(int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- getYPlane_float(int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- getZero(int, int) - Method in class features.ComputeCurvatures.FloatArray2D
-
- getzMax() - Method in interface adt.Byte3DArray
-
- getzMax() - Method in class adt.Sparse3DByteArray
-
- getzMax() - Method in class adt.Unsparse3DByteArray
-
- getzMin() - Method in interface adt.Byte3DArray
-
- getzMin() - Method in class adt.Sparse3DByteArray
-
- getzMin() - Method in class adt.Unsparse3DByteArray
-
- getZPlane(int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- getZPlane_float(int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- Gradient - Class in process3d
-
- Gradient() - Constructor for class process3d.Gradient
-
- GREY - Static variable in class vib.app.Options
-
- GreyTransformation - Class in vib.app.module
-
- GreyTransformation() - Constructor for class vib.app.module.GreyTransformation
-
- guessEulerParameters(double[]) - Method in class vib.FastMatrix
-
- guessEulerParameters(double[], Point3d) - Method in class vib.FastMatrix
-
- guessEulerParameters(float[]) - Method in class vib.FloatMatrix
-
- guessEulerParameters(float[], Point3d) - Method in class vib.FloatMatrix
-
- guessLevelFromWidth(int) - Static method in class vib.RigidRegistration
-
- gui - package gui
-
- GuiBuilder - Class in gui
-
- GuiBuilder() - Constructor for class gui.GuiBuilder
-
- SampleSphereSurface(double, double) - Static method in class vib.edge.SphereIterators
-
- SampleSphereSurface(double, double, double) - Static method in class vib.edge.SphereIterators
-
- save(String) - Method in class landmarks.NamePoints
-
- save(ImagePlus, String) - Method in class vib.app.module.State
-
- save(String, String) - Method in class vib.PointList
-
- save(PrintStream, boolean) - Method in class vib.PointList
-
- save - Variable in class vib.ShowHistogram
-
- saveAffineTransform(String, float[]) - Method in class math3d.TransformIO
-
- saveAffineTransform(float[]) - Method in class math3d.TransformIO
-
- saveIGSPointsFile(String) - Method in class landmarks.NamedPointSet
-
- savePointsFile(String) - Method in class landmarks.NamedPointSet
-
- saveTo(String) - Method in class vib.app.ImageMetaData
-
- saveTo(String) - Method in class vib.app.Options
-
- scalar(Point3d) - Method in class math3d.Point3d
-
- scale(double, double, double) - Method in class vib.FastMatrix
-
- scale(float, float, float) - Method in class vib.FloatMatrix
-
- scale(double, double, double) - Method in class vib.transforms.FastMatrixTransform
-
- scoreTransformation(ImagePlus, ImagePlus, int) - Method in class vib.transforms.OrderedTransformations
-
- scoreTransformation(ImagePlus, ImagePlus, BoundsInclusive) - Method in class vib.transforms.OrderedTransformations
-
- scoreTransformation(ImagePlus, ImagePlus, int, BoundsInclusive) - Method in class vib.transforms.OrderedTransformations
-
- scoreTransformationReal(ImagePlus, ImagePlus, int, BoundsInclusive) - Method in class vib.transforms.OrderedTransformations
-
- scoreTransformationThresholded(ImagePlus, ImagePlus, Threshold, Threshold, BoundsInclusive) - Method in class vib.transforms.OrderedTransformations
-
- scoreTransformationThresholded(ImagePlus, ImagePlus, Threshold, Threshold) - Method in class vib.transforms.OrderedTransformations
-
- scoreTransformationThresholded(ImagePlus, ImagePlus, Threshold, Threshold, int) - Method in class vib.transforms.OrderedTransformations
-
- scoreTransformationThresholdedReal(ImagePlus, ImagePlus, Threshold, Threshold, int, BoundsInclusive) - Method in class vib.transforms.OrderedTransformations
-
- searchInitialEulerParams() - Method in class vib.RegistrationOptimizer
-
- segment(SegmentatorModel) - Method in class oldsegmenters.AutoLabeller
-
- segment(SegmentatorModel) - Method in class oldsegmenters.AutoLabellerNaive
-
- SegmentationEditor - Class in vib.segment
-
Segmentation_Editor : ImageJ plugin.
- SegmentationEditor() - Constructor for class vib.segment.SegmentationEditor
-
- SegmentationViewerCanvas - Class in vib
-
- SegmentationViewerCanvas(ImagePlus) - Constructor for class vib.SegmentationViewerCanvas
-
- SegmentationViewerCanvas(ImagePlus, ImagePlus) - Constructor for class vib.SegmentationViewerCanvas
-
- SegmentatorModel - Class in oldsegmenters
-
Wrapper clas for an ImagePlus, stored vairous objects in the properties of the Image plus
OBjects used for segmentating
User: Tom Larkworthy
Date: 21-Jun-2006
Time: 00:08:57
- SegmentatorModel(ImagePlus) - Constructor for class oldsegmenters.SegmentatorModel
-
- select(int) - Method in class vib.segment.MaterialList
-
- set(float, int, int) - Method in class features.ComputeCurvatures.FloatArray2D
-
- set(float, int, int, int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- set - Variable in class landmarks.NamedPointWorld
-
- set(double, double, double) - Method in class landmarks.NamedPointWorld
-
- set(long, byte) - Method in class util.FindConnectedRegions.PointState
-
- set(double, double, double) - Method in class vib.BenesNamedPoint
-
- set(int, int, int, int) - Method in class vib.InterpolatedImage
-
- setActionCommand(String) - Method in class vib.segment.ImageButton
-
- setArmedBorder(Border) - Method in class vib.segment.ImageButton
-
Sets the border to display when the button is pressed and the mouse
is still over the button.
- setArmedImage(Image) - Method in class vib.segment.ImageButton
-
Sets the image to display when the button is pressed and the mouse
is still over the button.
- setBackground(Color) - Method in class vib.segment.MaterialList
-
- setBackground(Color) - Method in class vib.segment.Sidebar
-
- setBorder(Color) - Method in class vib.segment.Border
-
Sets the current border color.
- setBorderThickness(int) - Method in class vib.segment.Border
-
Sets the border thickness
- setBottomMargin(int) - Method in class vib.segment.Border
-
Sets the bottom margin
- setButtonState(int) - Method in class vib.segment.ImageButton
-
Sets the current buttonState id for the button
- setCalibration(ImagePlus) - Method in class amira.AmiraParameters
-
- setCalibration(Calibration) - Method in class amira.AmiraParameters
-
- setColor(int, int, int) - Method in class vib.segment.MaterialList
-
- setCropAbove(double) - Method in class stacks.ThreePaneCrop
-
- setCropBounds(int, int, int, int) - Method in class stacks.ThreePaneCropCanvas
-
- setCropCuboid(int, int, int, int, int, int) - Method in class stacks.ThreePaneCrop
-
- setCrosshairs(int, int, int, boolean) - Method in class landmarks.ProgressCanvas
-
- setCrosshairs(double, double, double, boolean) - Method in class stacks.ThreePanesCanvas
-
- setCurrentMaterial(AmiraParameters.Material) - Method in class oldsegmenters.SegmentatorModel
-
- setCurrentSlice(int) - Method in class vib.segment.CustomStackWindow
-
- setData(int[]) - Method in class inference.BEPBInference
-
- setData(Vector) - Method in class inference.BEPBInference
-
- setData(int[]) - Method in class inference.Inference
-
- setData(Vector) - Method in class inference.Inference
-
- setData(int[]) - Method in class inference.MAPInference
-
- setData(Vector) - Method in class inference.MAPInference
-
- setDefaultTemplate() - Method in class landmarks.NamePoints
-
- setDefaultTemplate(String) - Method in class landmarks.NamePoints
-
- setDisabledBorder(Border) - Method in class vib.segment.ImageButton
-
Sets the border to display when the button is disabled.
- setDisabledImage(Image) - Method in class vib.segment.ImageButton
-
Sets the image to display when the button is disabled.
- setFileGroup(FileGroup) - Method in class util.RohlfingSBA
-
- setFloat(int, int, int, float) - Method in class vib.InterpolatedImage
-
- setFromFlatDoubleArray(double[]) - Method in class vib.FastMatrix
-
- setFromFlatFloatArray(float[]) - Method in class vib.FloatMatrix
-
- setImages(ImagePlus, ImagePlus) - Method in class vib.oldregistration.RegistrationAlgorithm
-
- setInitialTransformation(double[]) - Method in class landmarks.FineTuneThread
-
- setInt(int, int, int, int) - Method in class vib.InterpolatedImage
-
- setLabelCanvas(SegmentationViewerCanvas) - Method in class oldsegmenters.SegmentatorModel
-
- setLabelImage(ImagePlus) - Method in class vib.segment.Sidebar
-
- setLabelImagePlus(ImagePlus) - Method in class oldsegmenters.SegmentatorModel
-
- setLabels(ImagePlus) - Method in class vib.segment.CustomStackWindow
-
- setLabels(ImagePlus) - Method in class vib.SegmentationViewerCanvas
-
- setLeftMargin(int) - Method in class vib.segment.Border
-
Sets the left margin
- setListener(SigmaPalette.SigmaPaletteListener) - Method in class features.SigmaPalette
-
- setMagnification(double) - Method in class vib.segment.CustomCanvas
-
- setMargins(int) - Method in class vib.segment.Border
-
Sets all margins (top, left, bottom, and right) to the same, given value.
- setMargins(int, int, int, int) - Method in class vib.segment.Border
-
Sets all margins (top, left, bottom, and right) to the given values.
- setMaterial(String, int, double, double, double, double) - Method in class vib.app.ImageMetaData
-
- setMaterials(String) - Method in class vib.segment.MaterialList
-
- setMatrix(String, FloatMatrix) - Method in class vib.app.ImageMetaData
-
- setMax(double) - Method in class features.SigmaPalette
-
- setName(String) - Method in class landmarks.NamedPointWorld
-
- setNewArrow(Arrow) - Method in interface util.ArrowDisplayer
-
- setNoInsets() - Method in class vib.segment.Border
-
sets all margins and thicknesses to zero
- setOriginalFile(File) - Method in class util.CMTKTransformation
-
- setOverBorder(Border) - Method in class vib.segment.ImageButton
-
Sets the border to display when the button is not pressed and the mouse
is over the button.
- setOverImage(Image) - Method in class vib.segment.ImageButton
-
Sets the image to display when the button is not pressed and the mouse
is over the button.
- setPaneOwner(PaneOwner) - Method in class stacks.ThreePanesCanvas
-
- setParameters(ImagePlus) - Method in class amira.AmiraParameters
-
- setParameters(ImagePlus, boolean) - Method in class amira.AmiraParameters
-
- setParameters(Properties) - Method in class amira.AmiraParameters
-
- setRightMargin(int) - Method in class vib.segment.Border
-
Sets the right margin
- setRoi(int, Roi) - Method in class vib.segment.CustomStackWindow
-
- setRoi(int, Roi, boolean) - Method in class vib.segment.CustomStackWindow
-
- setSelectedSigmaIndex(int) - Method in class features.SigmaPalette
-
- setShort(int, int, int, short) - Method in class vib.InterpolatedImage
-
- setSigma(double) - Method in class features.HessianEvalueProcessor
-
- setSlice(int, ImageProcessor) - Method in class video.VideoStack
-
- setSlicesAllPanes(int, int, int) - Method in class stacks.ThreePaneContainer
-
- setSlicesAllPanes(int, int, int) - Method in class stacks.ThreePanes
-
- setTopMargin(int) - Method in class vib.segment.Border
-
Sets the top margin
- setTransformation(FastMatrix) - Method in class vib.TransformedImage
-
- setTransformationMethod(String) - Method in class vib.app.Options
-
- setTranslation(double, double, double) - Method in class vib.transforms.FastMatrixTransform
-
- setType(int) - Method in class vib.segment.Border
-
Sets the border type (e.g., to Border.LINE)
- setUnarmedBorder(Border) - Method in class vib.segment.ImageButton
-
Sets the border to display when the button is not pressed or hilited
because of a mouse-over.
- setUnarmedImage(Image) - Method in class vib.segment.ImageButton
-
Sets the image to display when the button is not pressed or hilited
because of a mouse-over.
- setup() - Method in class features.ComputeCurvatures
-
- setup(String, ImagePlus) - Method in class oldsegmenters.LabelBinaryOps
-
- setup() - Method in class vib.ShowHistogram
-
- setXPlane(ComputeCurvatures.FloatArray2D, int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- setXPlane(float[][], int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- setYPlane(ComputeCurvatures.FloatArray2D, int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- setYPlane(float[][], int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- setZPlane(ComputeCurvatures.FloatArray2D, int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- setZPlane(float[][], int) - Method in class features.ComputeCurvatures.FloatArray3D
-
- show() - Method in class amira.AmiraTable
-
- show(int) - Method in class landmarks.NamePoints
-
- Show - Class in vib.app.module
-
- Show() - Constructor for class vib.app.module.Show
-
- showBinary - Variable in class vib.segment.Thresholder
-
- showDialog() - Method in class vib.app.gui.ProgressIndicator
-
- ShowHistogram - Class in vib
-
This class is an extended ImageWindow that displays histograms.
- ShowHistogram(double[], double, double) - Constructor for class vib.ShowHistogram
-
Displays a histogram using the title "Histogram of ImageName".
- ShowHistogram(long[], int) - Constructor for class vib.ShowHistogram
-
- showHistogram(double, double) - Method in class vib.ShowHistogram
-
Draws the histogram using the specified title and ImageStatistics.
- showList() - Method in class vib.ShowHistogram
-
- showProgress - Variable in class vib.TransformedImage.Iterator
-
- showProgress(int, int) - Static method in class vib.VIB
-
- showStatus(String) - Static method in class vib.VIB
-
- Sidebar - Class in vib.segment
-
Sidebar:
This class builds all the interface of the SegmentationEditor.
- Sidebar(CustomCanvas, ActionListener) - Constructor for class vib.segment.Sidebar
-
- sigma - Variable in class features.ComputeCurvatures
-
- sigma - Variable in class features.HessianEvalueProcessor
-
- SigmaPalette - Class in features
-
- SigmaPalette() - Constructor for class features.SigmaPalette
-
- SigmaPalette.PaletteCanvas - Class in features
-
- SigmaPalette.PaletteStackWindow - Class in features
-
- SigmaPalette.SigmaPaletteListener - Interface in features
-
- sigmaPaletteClosing() - Method in interface features.SigmaPalette.SigmaPaletteListener
-
- sign(int) - Static method in class util.Bresenham3D
-
- Simplex - Class in delaunay
-
A Simplex is an immutable set of vertices (usually Pnts).
- Simplex(Collection) - Constructor for class delaunay.Simplex
-
Constructor.
- Simplex(Object[]) - Constructor for class delaunay.Simplex
-
Constructor.
- single_pane - Variable in class stacks.ThreePanes
-
- size() - Method in class delaunay.Simplex
-
- size() - Method in class delaunay.Triangulation
-
Size (# of Simplices) in Triangulation.
- size() - Method in class landmarks.NamedPointSet
-
- size(double[]) - Static method in class vib.FastMatrix
-
- size(float[]) - Static method in class vib.FloatMatrix
-
- size() - Method in class vib.PointList
-
- sizeSquared(double[]) - Static method in class vib.FastMatrix
-
- sizeSquared(float[]) - Static method in class vib.FloatMatrix
-
- SliceEvent - Class in events
-
- SliceEvent(ImagePlus) - Constructor for class events.SliceEvent
-
- SliceListener - Interface in events
-
- sliceNumberChanged(SliceEvent) - Method in interface events.SliceListener
-
- SliceWatcher - Class in events
-
enclosing class is just an adapter,
the main functionality is hidden in properties of the IP
it allows the user a space to add SliceListeners
- SliceWatcher(ImagePlus) - Constructor for class events.SliceWatcher
-
- Smooth - Class in process3d
-
Smoothes an ImagePlus, either uniformly or by Gaussian blur.
- Smooth() - Constructor for class process3d.Smooth
-
- smooth(ImagePlus, boolean, float, boolean) - Static method in class process3d.Smooth
-
- solve_cholesky(double[][], double[]) - Static method in class math3d.FastMatrixN
-
Solve Ax = b.
- solve_cholesky(float[][], float[]) - Static method in class math3d.FloatMatrixN
-
Solve Ax = b.
- solve_UL(double[][], double[]) - Static method in class math3d.FastMatrixN
-
- solve_UL(float[][], float[]) - Static method in class math3d.FloatMatrixN
-
- SortedHalfCircle(double) - Static method in class vib.edge.CircleIterators
-
- sourceImages - Variable in class vib.oldregistration.RegistrationAlgorithm
-
- Sparse3DByteArray - Class in adt
-
allows 3D byte data to be stored effeciently, if the data is mostly 0s
User: Tom Larkworthy
Date: 12-Jul-2006
Time: 19:16:00
- Sparse3DByteArray() - Constructor for class adt.Sparse3DByteArray
-
- SphereIterator(double) - Static method in class vib.edge.SphereIterators
-
- SphereIterator(double, double) - Static method in class vib.edge.SphereIterators
-
- SphereIterator(double, double, double, double) - Static method in class vib.edge.SphereIterators
-
- SphereIterators - Class in vib.edge
-
- SphereIterators() - Constructor for class vib.edge.SphereIterators
-
- Spiral(Point) - Constructor for class oldsegmenters.Utils.Spiral
-
- SplitChannels - Class in vib.app.module
-
- SplitChannels() - Constructor for class vib.app.module.SplitChannels
-
- splitChannelsToArray(ImagePlus, boolean) - Static method in class util.BatchOpener
-
- sRGB2CIELAB(float[], float[]) - Static method in class color.CIELAB
-
- sRGB2int(float[]) - Static method in class color.CIELAB
-
- sRGB2XYZ(float[], float[]) - Static method in class color.CIELAB
-
- stacks - package stacks
-
- StackToFloatArray(ImageStack) - Method in class features.ComputeCurvatures
-
This method convertes an ImageJ image stack to my FloatArray3D,
which is a one dimensional structure with methods for 3D access
- stackWindow - Variable in class vib.segment.Thresholder
-
- start_x - Variable in class util.Arrow
-
- start_y - Variable in class util.Arrow
-
- start_z - Variable in class util.Arrow
-
- State - Class in vib.app.module
-
- State(Options) - Constructor for class vib.app.module.State
-
- Statistics(InterpolatedImage) - Constructor for class vib.app.module.TissueStatistics.Statistics
-
- stopFineTuneThreads() - Method in class landmarks.NamePoints
-
- StupidLog - Class in util
-
REMOVEME
Just a very temporary method, taken from BatchLog_.java and made less
useful :(
- StupidLog() - Constructor for class util.StupidLog
-
- subEvidences - Variable in class inference.BEPBInference
-
- subEvidences - Variable in class inference.Inference
-
- subEvidences - Variable in class inference.MAPInference
-
- subtract(Pnt) - Method in class delaunay.Pnt
-
Subtract.
- SurfacenessProcessor - Class in features
-
- SurfacenessProcessor(boolean) - Constructor for class features.SurfacenessProcessor
-
- SurfacenessProcessor(double, boolean) - Constructor for class features.SurfacenessProcessor
-
- synchronousRequest(Hashtable, byte[]) - Method in class client.ArchiveClient
-