BIJ API
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

a - Variable in class bijnum.BIJpca
The matrix of images.
a - Variable in class bijnum.BIJJacobi
The matrix of which you want to compute E.
abs(float[]) - Static method in class bijnum.BIJmatrix
Return a vector with the absolutes of all elements in vector v.
accept(File) - Method in class io.DirFilter
 
accuracy(float[], float[], int) - Static method in class bijnum.BIJstats
Compute accuracy of a test for which the result is in exp and the ground truth in truth, for class c.
accuracyMultipleClasses(float[], float[], int) - Static method in class bijnum.BIJstats
Compute the accuracy of a test of which the result is in exp and the ground truth in truth, where test results in multiple classifications.
actionPerformed(ActionEvent) - Method in class FlowJ.FlowJUserInterface
 
actionPerformed(ActionEvent) - Method in class VolumeJ.VJUserInterface
React to action e.
actionPerformed(ActionEvent) - Method in class io.OpenPreviewDialog
 
activateButtons(int) - Method in class VolumeJ.VJUserInterface
Activate the rendering buttons, depending on whether or not there is a stack, an image, or nothing available.
activateButtons(int) - Method in class VolumeJ.VJSurfaceJ
Activate the rendering and surface plot buttons, depending on whether or not there is a stack, an image, or nothing available.
add(float[][], double) - Static method in class bijnum.BIJmatrix
Add a scalar to all entries in a matrix m in place.
add(float[][], float[][]) - Static method in class bijnum.BIJmatrix
Add (elements in) a matrix b to a matrix a.
add(float[][], float[][], float[][]) - Static method in class bijnum.BIJmatrix
Add the elements of two matrices a and b and save the results in a matrix r.
add(float[], float, float[]) - Static method in class bijnum.BIJmatrix
 
add(short[], float) - Static method in class bijnum.BIJShortMatrix
Add a scalar to all entries in a matrix.
add(SSD, SSD) - Method in class FlowJ.SSD
 
add(VolumeFloat) - Method in class volume.VolumeFloat
 
addElements(double[], double[], double[]) - Static method in class bijnum.BIJmatrix
 
addElements(float[], float[]) - Static method in class bijnum.BIJmatrix
 
addElements(float[], float[], float[]) - Static method in class bijnum.BIJmatrix
 
addPathTree(Vector, File) - Method in class io.OpenPreviewDialog
Add the whole path for File current to the end of v.
advanceInit(VJCell, double, double, double) - Method in class VolumeJ.VJBinaryShell
Initialization of depth search routine.
advancePrepare(double, double, double) - Method in class VolumeJ.VJBinaryShell
Prepare surface search for a ray with a specific direction vector.
advanceToSurface(VJCell) - Method in class VolumeJ.VJBinaryShell
Advance a cell to a surface along the ray.
advanceToSurfaceTracing(VJCell) - Method in class VolumeJ.VJBinaryShell
Advance a cell to a surface along the ray.
almostOpaque() - Method in class VolumeJ.VJAlphaColor
Return whether this alphacolor is almost opaque.
alpha - Variable in class VolumeJ.VJAlphaColor
 
alpha - Variable in class of3d.OF3DSpot
 
alphacolor(FlowJValue, VJGradient) - Method in class of3d.OFClassifier
 
alphacolor(FlowJValue, VJGradient) - Method in class of3d.OFClassifierScintillans
Classify a flow based on the flow vector, and whether or not a static voxel is present, into a VJAlphaColor.
alphacolor(FlowJValue, VJGradient) - Method in class of3d.OFClassifierScintillansNoStatic
Classify a flow based on the flow vector, and whether or not a static voxel is present, into a VJAlphaColor.
alphacolor(FlowJValue, VJGradient) - Method in class of3d.OFClassifierDCM3DNoGradient
Classify a flow based on the flow vector, and whether or not a static voxel is present, into a VJAlphaColor.
alphacolor(FlowJValue, VJGradient) - Method in class of3d.OFClassifierScintillansIx255
Classify a flow based on the flow vector, and whether or not a static voxel is present, into a VJAlphaColor.
alphacolor(FlowJValue, VJGradient) - Method in class of3d.OFClassifierScintillansNoFlow
Classify flow value based on the flow vector, and whether or not a static voxel is present, into a VJAlphaColor.
alphacolor(FlowJValue, VJGradient) - Method in class of3d.OFClassifierDCM2DNoGradient
Classify a flow based on the flow vector, and whether or not a static voxel is present, into a VJAlphaColor.
alphacolor(FlowJValue, VJGradient) - Method in class of3d.OFClassifierScintillansIxLT0
Classify a flow based on the flow vector, and whether or not a static voxel is present, into a VJAlphaColor.
alphacolor(VJrgbValue, VJGradient) - Method in class VolumeJ.VJClassifierRGB
 
alphacolor(VJValue) - Method in class VolumeJ.VJClassifier
This method can be overloaded as necessary.
alphacolor(VJValue) - Method in class VolumeJ.VJClassifierLevoy
Slice view classification.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifier
The classification method, defining how a value/gradient combination will be classified as an VJAlphaColor (argb).
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierInteger
 
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierIsosurface
Classify the voxel value into RGB.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierLevoy
Classify the (interpolated) voxel value and gradient magnitude into a alpha and rgb-value.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierGradientCT
Classify the (interpolated) voxel value and gradient magnitude into a alpha and rgb-value.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierValue
Classify the interpolated voxel value into a VJAlphaColor.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierLevoyCueing
Classify the (interpolated) voxel value and gradient magnitude into a alpha and rgb-value.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierLNoIndex
 
alphacolor(VJValue, VJGradient) - Method in class of3d.OFClassifier
 
alphacolorFlow(float[]) - Method in class of3d.OFClassifierScintillans
Classify a flow based on the flow vector into a VJAlphaColor.
an - Variable in class bijnum.BIJpca
 
aspectField - Variable in class VolumeJ.VJUserInterface
 
aspectx - Static variable in class VolumeJ.VJUserInterface
 
aspectx - Variable in class volume.Volume
Anisotropy measure of the volume.
aspecty - Static variable in class VolumeJ.VJUserInterface
 
aspecty - Variable in class volume.Volume
Anisotropy measure of the volume.
aspectz - Static variable in class VolumeJ.VJUserInterface
 
aspectz - Variable in class volume.Volume
Anisotropy measure of the volume.
at(int, int, int) - Method in class VolumeJ.VJShape
 
attenuate(VJShade) - Method in class VolumeJ.VJAlphaColor
 
average(Roi) - Method in class FlowJ.FlowJError
 
average(Roi) - Method in class FlowJ.FlowJFlow
 
averageAlpha() - Method in class FlowJ.FlowJFlow
Return the angle of the previously computed average flow.
averageMagnitude() - Method in class FlowJ.FlowJFlow
Return the length of the previously computed average flow.
averageOverVelocity() - Method in class FlowJ.FlowJError
 
avg(float[]) - Static method in class bijnum.BIJstats
Compute average of all values in vector v.
avg(float[], float[]) - Static method in class bijnum.BIJstats
 
avgNoExtremes(float[], float) - Static method in class bijnum.BIJstats
 
axes - Variable in class FlowJ.FlowJMapper
 
axes - Variable in class of3d.OFClassifierScintillans
 
axisChoice - Variable in class VolumeJ.VJUserInterface
 

B

b - Variable in class VolumeJ.VJAlphaColor
 
b - Variable in class VolumeJ.VJrgbValue
 
b - Variable in class volume.VolumeRGB
The brightness of each voxel as a byte (0-225).
backCheckbox - Variable in class VolumeJ.VJUserInterface
 
backproject(Volume) - Method in class VolumeJ.VJProjection
Backprojection around a single axis y.
bcomposite - Static variable in class FlowJ.FlowJSpotNoise
 
Beaudetx - class volume.Beaudetx.
This class implements Beaudet differentiation in x direction.
Beaudetx() - Constructor for class volume.Beaudetx
Initialize Beaudet kernel.
betacf(double, double, double) - Static method in class bijnum.BIJfunctions
 
betai(double, double, double) - Static method in class bijnum.BIJfunctions
 
BIJException - exception bijnum.BIJException.
 
BIJException() - Constructor for class bijnum.BIJException
 
BIJException(int) - Constructor for class bijnum.BIJException
 
BIJException(String) - Constructor for class bijnum.BIJException
 
BIJfht - class bijnum.BIJfht.
This class implements the fast Hartley transform on images (real float matrices).
BIJfht(int) - Constructor for class bijnum.BIJfht
Set up a BIJfht for matrices of size length = maxNxmaxN
BIJfunctions - class bijnum.BIJfunctions.
20-July-1997, Bryan Lewis, Department of Mathematics and Computer Science, Kent State University (*) Press, Flannery, Teukolsky, Vetterling, Numerical Recipes, Cambridge University Press, 1986
BIJfunctions() - Constructor for class bijnum.BIJfunctions
 
BIJgifa - class bijnum.BIJgifa.
Implementation of GIFA (generalized indicator function approach).
BIJgifa() - Constructor for class bijnum.BIJgifa
 
BIJJacobi - class bijnum.BIJJacobi.
This class implements the jacobi function as a Java class.
BIJJacobi(float[][]) - Constructor for class bijnum.BIJJacobi
Create new instance to compute eigenvectors, eigenvalues.
BIJJacobi(float[][], boolean) - Constructor for class bijnum.BIJJacobi
Create new instance to compute eigenvectors, eigenvalues.
BIJknn - class bijnum.BIJknn.
k Nearest Neighborhood (brute-force) implementation.
BIJknn(float[][], float[], int) - Constructor for class bijnum.BIJknn
 
BIJmatrix - class bijnum.BIJmatrix.
Implements methods for large (by necessity, float) matrices, including covariance of matrix, eigenvectors and others.
BIJmatrix() - Constructor for class bijnum.BIJmatrix
 
BIJmi - class bijnum.BIJmi.
Mutual infromation processing routines.
BIJmi(float, float, float) - Constructor for class bijnum.BIJmi
 
bijnum - package bijnum
 
BIJpca - class bijnum.BIJpca.
Principal component analysis (PCA) on 2-D sequences (ie.
BIJpca() - Constructor for class bijnum.BIJpca
Set up PCA.
BIJpca(float[][], float[][]) - Constructor for class bijnum.BIJpca
Set up PCA for already computed coordinates and eigenimages.
BIJpowell - class bijnum.BIJpowell.
This class implements Powell's multidimensional optimization.
BIJpowell() - Constructor for class bijnum.BIJpowell
 
BIJShortMatrix - class bijnum.BIJShortMatrix.
Implements methods for large short matrices.
BIJShortMatrix() - Constructor for class bijnum.BIJShortMatrix
 
BIJstats - class bijnum.BIJstats.
BIJ statistical methods inherited from MatLab.
BIJstats() - Constructor for class bijnum.BIJstats
 
BIJtransform - class bijnum.BIJtransform.
This class implements static transformation matrix operations for 2-D and 3-D transformation matrices.
BIJtransform() - Constructor for class bijnum.BIJtransform
 
BIJutil - class bijnum.BIJutil.
Utilities to link BIJ things to ImageJ.
BIJutil() - Constructor for class bijnum.BIJutil
 
bilinear(float[], int, float, float) - Static method in class volume.Transformer
Bilinearly interpolate the pixel at x,y.
bilinearExtend(float[], int, int, float, float) - Static method in class volume.Transformer
Interpolate the pixel at x,y in image, extend if x,y not in image .
binIndex(int[], float) - Static method in class bijnum.BIJstats
Compute the lowest bin into which the highest p percent of occurrences falls.
bins - Variable in class bijnum.BIJmi
 
bitrev - Variable in class bijnum.BIJfht
 
BitRevRArr(float[], int, int, int) - Method in class bijnum.BIJfht
 
bl(float[][][], int, int, float, float) - Static method in class FlowJ.FlowJMapper
This is a HACK and should not be here.
Blas - class bijnum.Blas.
 
Blas() - Constructor for class bijnum.Blas
 
blb - Variable in class VolumeJ.VJVoxelLoc
 
blendCompose(int, VJValue, VJGradient, VJAlphaColor, VJShade) - Method in class VolumeJ.VJViewspaceRender
Compose the classified voxel color into pixel.
blendCompose(int, VJValue, VJGradient, VJAlphaColor, VJShade) - Method in class of3d.FlowJScintillansRender
Compose the classified voxel color into pixel.
blendCompose(VJAlphaColor, VJValue, VJGradient, VJAlphaColor, VJShade) - Method in class VolumeJ.VJRender
Compose the classified voxel color into pixel.
blendComposeScalar(VJAlphaColor, VJShade) - Method in class VolumeJ.VJAlphaColor
Composing.
blendComposeVector(int, FlowJValue, VJGradient, VJAlphaColor, VJShade) - Method in class of3d.FlowJScintillansRender
Scintillans rendering shows (a subset of) the vectors as halved, small colored elongated oriented Gaussian stretches (scintillations).
blf - Variable in class VolumeJ.VJVoxelLoc
 
bp - Static variable in class FlowJ.FlowJSpotNoise
 
brb - Variable in class VolumeJ.VJVoxelLoc
 
brf - Variable in class VolumeJ.VJVoxelLoc
 
buildAngles(double, int) - Method in class VolumeJ.VJProjection
Compute the angle of each projection image for a sequence of equidistant projection images.

C

C - Variable in class bijnum.BIJfht
Static variables used in BIJfht algorithms.
calcpsi(OF3DFlow) - Method in class of3d.OF3DFlow
 
calcpsiRotation(int, int, float) - Method in class of3d.OF3DFlow
 
calcpsiTranslation(float, float, float) - Method in class of3d.OF3DFlow
 
calibratedMagnitudeString(float, int) - Method in class FlowJ.FlowJFlow
 
cancel - Variable in class io.OpenPreviewDialog
 
canceling - Variable in class io.OpenPreviewDialog
Whether you are canceling at end of dialog.
canListRoots - Variable in class io.OpenPreviewDialog
 
center(float[], int, float[], int, float) - Static method in class bijnum.BIJutil
Center a scaled image1 into the center of a larger image0.
center(SSD, int[]) - Method in class FlowJ.SSD
 
center(VJMatrix, Volume) - Static method in class VolumeJ.VJRenderView
Center m around 0,0,0 by translating to the center of the volume.
centerVolume(Volume, VJMatrix) - Method in class VolumeJ.VJViewspaceUtil
Determine the center of volume v in coordinate system m.
CentralDiff - class volume.CentralDiff.
This class implements a four point central difference gradient kernel.
CENTRALDIFF - Static variable in class FlowJ.FlowJLucas
 
CentralDiff() - Constructor for class volume.CentralDiff
 
chance - Static variable in class FlowJ.Flow3JColorNoiseMapper
 
chance - Static variable in class FlowJ.FlowJColorNoiseMapper
 
chance - Static variable in class FlowJ.FlowJSpotNoiseMapper
 
channels() - Method in class VolumeJ.VJShade
 
check(double[][]) - Method in class bijnum.Jacobi
Deprecated.  
check(float, float, float, float, float, float, float) - Static method in class VolumeJ.VJPlane
Return the result of a plane equation with a,b,c,d with a point x,y,z filled in.
check(int, int, int[], float) - Method in class FlowJ.SSD
 
checkinverse(double[][], double[][]) - Static method in class bijnum.BIJmatrix
Check whether JI is really the inverse of J.
choiceDir - Variable in class io.OpenPreviewDialog
 
CI95 - Static variable in class bijnum.BIJstats
Conversion from standard error to confidence intervals at different significance levels.
CI99 - Static variable in class bijnum.BIJstats
 
CI99_9 - Static variable in class bijnum.BIJstats
 
cineField - Variable in class VolumeJ.VJUserInterface
 
cineNField - Variable in class VolumeJ.VJUserInterface
 
classes - Static variable in class VolumeJ.VJClassifiers
 
classificationChoice - Variable in class VolumeJ.VJUserInterface
 
classifier - Variable in class VolumeJ.VJRenderer
Voxel classifier.
classifier - Variable in class VolumeJ.VJUserInterface
 
classifierTextArea - Variable in class VolumeJ.VJUserInterface
 
classify(float[], float[][], int) - Method in class bijnum.BIJknn
Find the classification of all M (N dimensional) vectors unknown in the dataset.
classset - Variable in class bijnum.BIJknn
The classification for each element in the dataset, a 1xM vector.
clean() - Method in class bijnum.BIJknn
Cleans the dataset using Wilson's pruning algorithm.
clean(double) - Static method in class bijnum.BIJtransform
 
clickTime - Variable in class VolumeJ.VJViewerCanvas
Some practical variables
clipboard(PrintWriter) - Method in class FlowJ.FlowJError
 
col(float[][], int) - Static method in class bijnum.BIJmatrix
Return the n'th column of matrix m as a vector.
colaxpy_j(int, double, double[][], int, int, int) - Static method in class bijnum.Blas
This method multiplies a constant times a portion of a column of a matrix and adds the product to the corresponding portion of another column of the matrix --- a portion of col2 is replaced by the corresponding portion of a*col1 + col2.
coldot_j(int, double[][], int, int, int) - Static method in class bijnum.Blas
This method calculates the dot product of portions of two columns of a matrix.
colisamax_j(int, double[][], int, int, int) - Static method in class bijnum.Blas
This method finds the index of the element of a portion of a column of a matrix that has the maximum absolute value.
colnrm2_j(int, double[][], int, int) - Static method in class bijnum.Blas
This method calculates the Euclidean norm of a portion of a column of a matrix.
colorAlpha(byte[]) - Method in class VolumeJ.VJShape
 
COLORINT - Static variable in class VolumeJ.VJRenderer
Defines type of image the rendering is output to: color (as int).
ColorToInt(Color) - Static method in class volume.VolumeRGB
Utility routine to convert a java Color to an ARGB int.
colrot_j(int, double[][], int, int, double, double) - Static method in class bijnum.Blas
This method "applies a plane rotation." It is a modification of the LINPACK function DROT.
colscal_j(int, double, double[][], int, int) - Static method in class bijnum.Blas
This method scales a portion of a column of a matrix by a constant.
colswap_j(int, double[][], int, int) - Static method in class bijnum.Blas
This method interchanges two columns of a matrix.
colvaxpy_j(int, double, double[][], double[], int, int) - Static method in class bijnum.Blas
This method multiplies a constant times a portion of a column of a matrix x[ ][ ] and adds the product to the corresponding portion of a vector y[ ] --- a portion of y[ ] is replaced by the corresponding portion of ax[ ][j] + y[ ].
colvdot_j(int, double[][], double[], int, int) - Static method in class bijnum.Blas
This method calculates the dot product of a portion of a column of a matrix and the corresponding portion of a vector.
colvraxpy_j(int, double, double[], double[][], int, int) - Static method in class bijnum.Blas
This method multiplies a constant times a portion of a vector y[ ] and adds the product to the corresponding portion of a column of a matrix x[ ][ ] --- a portion of column j of x[ ][ ] is replaced by the corresponding portion of ay[ ] + x[ ][j].
compareTo(Object) - Method in class io.FileAndString
 
compose(VJAlphaColor, float) - Method in class VolumeJ.VJAlphaColor
Additive color mixing.
compose(VJAlphaColor, VJShade, float) - Method in class VolumeJ.VJAlphaColor
Additive shading and color mixing.
compute() - Method in class bijnum.BIJJacobi
Compute all eigenvalues and eigenvectors of a real symmetric matrix a[N][N].
compute() - Method in class volume.Diffusion
 
compute(double[][]) - Method in class bijnum.Jacobi
Deprecated.  
compute(float) - Method in class VolumeJ.VJShade
Compute the value of contribution after shading with this shade.
compute(float[][]) - Method in class bijnum.Jacobi
Deprecated.  
compute(float[][]) - Method in class bijnum.BIJpca
Compute the PCA.
compute(float[][], int) - Method in class bijnum.BIJgifa
Compute GIFA for k conditions.
compute(float[], boolean) - Method in class bijnum.BIJfht
Perform a Fast Hartley Transform on an image BIJfht of maxN x maxN pixels.
compute1(FlowJFlow, float) - Method in class FlowJ.FlowJSingh
 
compute2(FlowJFlow, float) - Method in class FlowJ.FlowJSingh
 
compute3D() - Method in class volume.Diffusion3D
 
compute4D() - Method in class volume.Diffusion3D
 
computed - Variable in class of3d.OF3DFlow
 
computeEigenimages() - Method in class bijnum.BIJpca
Compute the spatial eigenimages, i.e.
computeFull(FlowJFlow, boolean, float, float, int) - Method in class FlowJ.FlowJLucas
Compute full flow field from the first order gradients in dx, dy, dt for a weighted local neighborhood omega (weighted by G defined by sigmaw) around every image location.
computeFull(FlowJFlow, float, float) - Method in class FlowJ.FlowJFleet
Compute all full velocities from 5*5 neighbourhoods of normal velocities.
computeFull(FlowJFlow, int, float) - Method in class FlowJ.FlowJUras
 
computeLinearCombination() - Method in class bijnum.BIJpca
Compute the linear combination of all eigenimages.
computeLinearCombination(float[]) - Method in class bijnum.BIJpca
Compute a (compacted) linear combination of the imagevectors, using only with factor set to 1.
computeProbs(int) - Method in class bijnum.BIJmi
 
computeProjection(float[]) - Method in class bijnum.BIJpca
Compute the projection of a vector v onto the set of eigenimages.
computePsi(FlowJFlow, FlowJFlow) - Method in class FlowJ.FlowJError
 
computeSingleFrame(int) - Method in class FlowJ.FlowJUserInterface
Compute the flow from the current stack.
computeTransformationMatrix() - Method in class VolumeJ.VJRenderView
Fully calculate the transformation matrix for a view.
convertParametersIntoTransformationMatrix(double[]) - Static method in class volume.Transformer
Convert a bunch of double transformation parameters into a transformation matrix.
convertParametersIntoTransformationMatrix(float[]) - Static method in class volume.Transformer
Convert a bunch of float transformation parameters into a transformation matrix.
convertParametersIntoTransformationMatrix(float[], float, float) - Static method in class volume.Transformer
Convert a bunch of float transformation parameters into a transformation matrix.
Convolver - class volume.Convolver.
This class implements convolution operations on image planes and volumes.
Convolver() - Constructor for class volume.Convolver
 
convolvet(HyperVolume, Kernel1D) - Method in class volume.HyperVolume
Compute separated 1d convolution: hv=hv1*kernel in t dimension.
convolvet(HyperVolume, Kernel3D) - Method in class volume.HyperVolume
Compute separated 3d convolution: hv=hv1*kernel in t dimension.
convolvet(ImageStack, int, Kernel1D) - Method in class volume.VolumeFloat
Load a volume from a ImageStack, convert to float and do 1D z convolution on the fly.
convolvet(Kernel1D) - Method in class volume.HyperVolume
Compute separated 1d convolution: hv=hv1*kernel in t dimension in place.
convolvex(float[], int, int, int, Kernel1D) - Static method in class volume.Convolver
Convolution of float volume with symmetric 1D kernel in x dimension.
convolvex(float[], int, int, Kernel1D) - Static method in class volume.Convolver
Convolution of plane with 1D separated kernel along the x-axis.
convolvex(HyperVolume, Kernel1D) - Method in class volume.HyperVolume
Compute separated 1d convolution: v=v1*kernel in y dimension.
convolvex(HyperVolume, Kernel3D) - Method in class volume.HyperVolume
Compute separated 3d convolution: hv=hv1*kernel in x dimension.
convolvex(VolumeFloat, Kernel1D) - Method in class volume.VolumeFloat
 
convolvex(VolumeFloat, Kernel2D) - Method in class volume.VolumeFloat
 
convolvex(VolumeFloat, Kernel3D) - Method in class volume.VolumeFloat
 
convolvexy(float[], int, int, Kernel1D) - Static method in class volume.Convolver
Convolution of plane with 1D separated kernel.
convolvexy(float[], int, int, Kernel2D) - Static method in class volume.Convolver
Convolution of plane with symmetric 2D kernel in both directions.
convolvexy(Kernel1D) - Method in class volume.VolumeFloat
2D xy convolution separated over x and y.
convolvexy(Kernel2D) - Method in class volume.VolumeFloat
 
convolvexy(short[], int, int, Kernel1D) - Static method in class volume.Convolver
Convolution of plane with 1D separated kernel.
convolvexyz(float[], int, int, int, Kernel3D) - Static method in class volume.Convolver
Convolution of float volume with symmetric 3D kernel in all dimensions.
convolvexyz(Kernel1D) - Method in class volume.VolumeShort
XYZ convolution with separated 1D kernel.
convolvexyz(Kernel1D) - Method in class volume.VolumeFloat
XYZ convolution with separated 1D kernel.
convolvexyz(Kernel1D) - Method in class volume.HyperVolume
Convolve the hypervolume by kernel in xyz in place (so no extra hypervolume needed).
convolvexyz(Kernel3D) - Method in class volume.VolumeFloat
 
convolvexyz(short[], int, int, int, Kernel3D) - Static method in class volume.Convolver
Convolution of short volume with symmetric 3D kernel in all dimensions.
convolvey(float[], int, int, int, Kernel1D) - Static method in class volume.Convolver
Convolution of float volume with symmetric 1D kernel in y dimension.
convolvey(float[], int, int, Kernel1D) - Static method in class volume.Convolver
Convolution of plane with 1D separated kernel along the y-axis.
convolvey(HyperVolume, Kernel1D) - Method in class volume.HyperVolume
Compute separated 1d convolution: hv=hv1*kernel in y dimension.
convolvey(HyperVolume, Kernel3D) - Method in class volume.HyperVolume
Compute separated 3d convolution: hv=hv1*kernel in y dimension.
convolvey(VolumeFloat, Kernel1D) - Method in class volume.VolumeFloat
 
convolvey(VolumeFloat, Kernel2D) - Method in class volume.VolumeFloat
 
convolvey(VolumeFloat, Kernel3D) - Method in class volume.VolumeFloat
 
convolvez(float[], int, int, int, Kernel1D) - Static method in class volume.Convolver
Convolution of float volume with symmetric 1D kernel in x dimension.
convolvez(HyperVolume, Kernel1D) - Method in class volume.HyperVolume
Compute separated 1d convolution: hv=hv1*kernel in z dimension.
convolvez(HyperVolume, Kernel3D) - Method in class volume.HyperVolume
Compute separated 3d convolution: hv=hv1*kernel in z dimension.
convolvez(VolumeFloat) - Method in class volume.VolumeFloat
 
convolvez(VolumeFloat, Kernel1D) - Method in class volume.VolumeFloat
 
convolvez(VolumeFloat, Kernel2D) - Method in class volume.VolumeFloat
 
convolvez(VolumeFloat, Kernel3D) - Method in class volume.VolumeFloat
 
copy(float[]) - Static method in class bijnum.BIJmatrix
Copy a vector.
copy(float[][]) - Static method in class bijnum.BIJmatrix
Copy a matrix.
copy(short[]) - Static method in class bijnum.BIJShortMatrix
Copy a vector.
copy(VJAlphaColor) - Method in class VolumeJ.VJAlphaColor
Make a copy of this VJAlphaColor.
copy(VolumeFloat) - Method in class volume.VolumeFloat
 
copyToClipboard() - Method in class FlowJ.FlowJUserInterface
 
correction - Static variable in class FlowJ.FlowJSpotNoise
 
correl(float[], float[]) - Static method in class bijnum.BIJstats
Compute the correlation of a vector with another vector b.
covariance(float[][], boolean) - Static method in class bijnum.BIJstats
Compute the covariance matrix for a matrix of size NxM.
createChoice(Panel[], String, String[], int) - Method in class VolumeJ.VJUserInterface
Create a choice item, fill it with d strings and preselect item i.
createChoice(Panel, GridBagConstraints, GridBagLayout, String, String[], int) - Method in class VolumeJ.VJUserInterface
Create a choice item, fill it with d strings and preselect item i.
createChoice(Panel, String, String[], int) - Method in class VolumeJ.VJUserInterface
Create a choice item, fill it with d strings and preselect item i.
createRotation(int, int, float, Roi) - Method in class FlowJ.FlowJFlow
 
createTextField(Panel, GridBagConstraints, GridBagLayout, String, String, int) - Method in class VolumeJ.VJUserInterface
Create an entry item named s, with i characters in it.
createTextField(Panel, String, String, int) - Method in class VolumeJ.VJUserInterface
Create a text field with default content "d" of length i (in characters), labeled by "s".
createXYZField(Panel[], String, String[], int) - Method in class VolumeJ.VJUserInterface
 
createXYZField(Panel, String[], int) - Method in class VolumeJ.VJUserInterface
Create a series of text fields labeled with no label
createXYZField(Panel, String, String[], int) - Method in class VolumeJ.VJUserInterface
 
crop(float[], int, int, int, int, int, int) - Static method in class bijnum.BIJutil
Crop a float image to the rectangular size of a ROI defined by x,y,newwidth,newheight
crossPowerSpectrum(float[], float[]) - Method in class bijnum.BIJfht
Compute the conjugate product R = IM1* IM2 for real matrices (Hartley transformed) im1 and im2.
crossPowerSpectrum2(float[], float[], int) - Method in class bijnum.BIJfht
Alternative method to compute the cross power spectrum (im1* im2) / | im1 im2 | for Hartley (as opposed to Fourier) opposed matrices im1 and im2.
cutout - Variable in class VolumeJ.VJRenderer
 
cutout(VJAlphaColor, int, int, int) - Method in class VolumeJ.VJCutout
This routine decides whether to show a cutout slice or a rendered surface at pixel i,j.
cutoutCheckbox - Variable in class VolumeJ.VJUserInterface
 
cutoutField - Variable in class VolumeJ.VJUserInterface
 

D

dA(HyperVolume, int, int, int, int) - Static method in class volume.Diffusion3D
 
dataset - Variable in class bijnum.BIJknn
The dataset, a MxN matrix of N-dimensional vectors.
daxpy_j(int, double, double[], int, double[], int) - Static method in class bijnum.Blas
This method multiplies a constant times a vector and adds the product to another vector --- dy[ ] = da*dx[ ] + dy[ ].
dB(HyperVolume, int, int, int, int) - Static method in class volume.Diffusion3D
 
DCM2D - Static variable in class FlowJ.FlowJDisplay
 
DCM3D - Static variable in class FlowJ.FlowJDisplay
 
DCM3DNOISE - Static variable in class FlowJ.FlowJDisplay
 
dcmImage(FlowJFlow, ImageProcessor, float, float) - Static method in class FlowJ.FlowJDisplay
 
DCNOISE - Static variable in class FlowJ.FlowJDisplay
 
dcopy_j(int, double[], int, double[], int) - Static method in class bijnum.Blas
This method copies the vector dx[ ] to the vector dy[ ].
dcopyp_j(int, double[], double[], int) - Static method in class bijnum.Blas
This method copies a portion of vector x[ ] to the corresponding portion of vector y[ ].
dD(HyperVolume, int, int, int, int) - Static method in class volume.Diffusion3D
 
dD(VolumeFloat, int, int, int) - Static method in class volume.Diffusion3D
 
ddot_j(int, double[], int, double[], int) - Static method in class bijnum.Blas
This method calculates the dot product of two vectors.
dE(float[], int, int, int) - Static method in class volume.Diffusion
 
dE(HyperVolume, int, int, int, int) - Static method in class volume.Diffusion3D
 
dE(VolumeFloat, int, int, int) - Static method in class volume.Diffusion3D
 
debug - Variable in class FlowJ.FlowJUras
 
debug - Variable in class FlowJ.FlowJSingh
 
debug - Variable in class FlowJ.FlowJLucas
 
debug - Variable in class of3d.OF3DLucas
 
defaultDirectory - Static variable in class VolumeJ.VJUserInterface
 
defaultLUT() - Method in class VolumeJ.VJClassifierLevoy
Make a LUT obtained from a spectrum.
defaultLUT() - Method in class VolumeJ.VJClassifierLNotIndex0
Setup a default LUT.
defaultLUT() - Method in class VolumeJ.VJClassifierGradientCT
Fill the lut if not initialised from elsewhere.
defaultViewport() - Method in class VolumeJ.VJRenderer
Get a default viewport automatically.
delete(String) - Method in class volume.VolumeIO
 
Demodulation - class FlowJ.Demodulation.
 
Demodulation(float, boolean) - Constructor for class FlowJ.Demodulation
 
density - Variable in class FlowJ.FlowJLucas
 
depth - Variable in class VolumeJ.VJReconstructor
 
depth - Variable in class VolumeJ.VJRenderer
Boundaries of viewspace volume (the viewport) in k,j,i space.
depth - Variable in class of3d.OF3DDeformer
 
depth - Variable in class volume.Volume
Dimensions of the volume.
depth - Variable in class volume.Diffusion3D
 
desc() - Static method in class VolumeJ.VJIsosurfaceRender
 
desc() - Static method in class VolumeJ.VJViewspaceRender
 
desc() - Static method in class VolumeJ.VJRender
 
description - Static variable in class FlowJ.FlowJDisplay
 
description - Variable in class VolumeJ.VJClassifier
A short description of the classifier.
description - Variable in class VolumeJ.VJRenderView
 
description - Variable in class VolumeJ.VJRenderer
 
description - Static variable in class of3d.OF3DDisplay
 
det(float[], int, double) - Static method in class volume.Hessian
Compute the determinant of the Hessian matrix of image.
determinant(float[][]) - Static method in class bijnum.BIJmatrix
Compute determinant of m.
deviation - Static variable in class VolumeJ.VJUserInterface
 
dfht3(float[], int, boolean, int) - Method in class bijnum.BIJfht
 
diag(float[]) - Static method in class bijnum.BIJmatrix
Get a square matrix with v on the diagonal.
diag(float[][]) - Static method in class bijnum.BIJmatrix
Get the diagonal vector of (square) matrix m.
dialog - Variable in class io.OpenPreviewDialog
 
diffuse - Variable in class VolumeJ.VJLight
 
Diffusion - class volume.Diffusion.
This is a class that implements nonlinear diffusion in 2D.
Diffusion(ImagePlus) - Constructor for class volume.Diffusion
 
Diffusion3D - class volume.Diffusion3D.
This is a class that implements nonlinear diffusion in 2D, 3D and 4D.
Diffusion3D() - Constructor for class volume.Diffusion3D
 
directory - Static variable in class io.OpenPreviewDialog
 
DirFilter - class io.DirFilter.
 
DirFilter() - Constructor for class io.DirFilter
 
dirs - Variable in class io.OpenPreviewDialog
 
discoverEnvironment() - Method in class FlowJ.FlowJUserInterface
 
discreteSupport(Kernel) - Method in class volume.Volume
Returns the minimum depth needed to be able to filter (z-dimension) for the kernel.
discriminant(FlowJFlow, float[][], float[][], float[][]) - Method in class FlowJ.FlowJUras
 
diskCheckbox - Variable in class VolumeJ.VJUserInterface
 
displayon - Variable in class FlowJ.FlowJLucas
 
displayon - Variable in class of3d.OF3DLucas
 
distance(float[], float[]) - Static method in class bijnum.BIJknn
Return the distance according to some Minkowski metric.
distanceToAngle(int) - Method in class VolumeJ.VJViewerCanvas
Compute the angle corresponding to a mouse motion (in pixels) dx.
div(float[], double) - Static method in class bijnum.BIJmatrix
Divide each entry in v by divisor.
divElements(float[][], double) - Static method in class bijnum.BIJmatrix
Divide each entry in m by divisor.
divElements(float[], float[], float[]) - Static method in class bijnum.BIJmatrix
Divide all elements in vector a by elements in b.
dN(float[], int, int, int) - Static method in class volume.Diffusion
 
dN(HyperVolume, int, int, int, int) - Static method in class volume.Diffusion3D
 
dN(VolumeFloat, int, int, int) - Static method in class volume.Diffusion3D
 
dnrm2_j(int, double[], int) - Static method in class bijnum.Blas
This method calculates the Euclidean norm of the vector stored in dx[ ] with storage increment incx.
dnrm2p_j(int, double[], int) - Static method in class bijnum.Blas
This method calculates the Euclidean norm of a portion of a vector x[ ].
doBackface - Variable in class VolumeJ.VJShader
 
doCompute(boolean) - Method in class FlowJ.FlowJUserInterface
Compute the flow for a single or a range of frames in the stack.
doComputeFlow() - Method in class of3d.OF3DUserInterface
Do optic flow computation.
doComputeTestFlow() - Method in class of3d.OF3DUserInterface
 
doDepthCueing - Variable in class VolumeJ.VJRenderer
 
does() - Method in class VolumeJ.VJClassifier
Returns the type of VJAlphaColor this classifier generates: RGB or GRAYSCALE.
does() - Method in class VolumeJ.VJClassifierIsosurface
 
does() - Method in class VolumeJ.VJClassifierIsosurfaceGrayscale
 
does() - Method in class VolumeJ.VJClassifierLevoy
Tell calling program that this classifier will return RGB values.
does() - Method in class VolumeJ.VJClassifierLNoIndex
 
does() - Method in class VolumeJ.VJClassifierRGB
 
does() - Method in class of3d.OFClassifierScintillans
 
doesCutouts() - Method in class VolumeJ.VJClassifier
This method can be overloaded as necessary.
doesCutouts() - Method in class VolumeJ.VJClassifierIsosurface
 
doesCutouts() - Method in class VolumeJ.VJClassifierLevoy
Tells the calling program it can process cutouts (slice faces).
doesIndex() - Method in class VolumeJ.VJClassifier
Tell renderer whether this classifier can process indices in the voxel value.
doesIndex() - Method in class VolumeJ.VJClassifierIsosurface
 
doesIndex() - Method in class VolumeJ.VJClassifierLevoy
Tells renderer this classifier can process indices in the voxel values.
doesIndex() - Method in class VolumeJ.VJClassifierValue
 
doesIndex() - Method in class VolumeJ.VJClassifierLNoIndex
 
doesIndex() - Method in class VolumeJ.VJClassifierRGB
 
doesIndex() - Method in class of3d.OFClassifierScintillans
 
doesIndex() - Method in class of3d.OFClassifierScintillansNoStatic
 
doesIndex() - Method in class of3d.OFClassifierDCM3DNoGradient
 
doesIndex() - Method in class of3d.OFClassifierScintillansIx255
 
doesIndex() - Method in class of3d.OFClassifierScintillansNoFlow
 
doesIndex() - Method in class of3d.OFClassifierDCM2DNoGradient
 
doesIndex() - Method in class of3d.OFClassifierScintillansIxLT0
 
doesStatic() - Method in class of3d.OFClassifier
 
doesStatic() - Method in class of3d.OFClassifierScintillans
 
doesStatic() - Method in class of3d.OFClassifierScintillansNoStatic
 
doFeedback - Variable in class bijnum.BIJJacobi
Whether to show a showProgress() in ImageJ only.
doFlatFlow(OF3DFlow) - Method in class of3d.OF3DUserInterface
 
DoG - class volume.DoG.
This is a 1D Difference of Gaussian convolution kernel.
DoG(double) - Constructor for class volume.DoG
Create a Difference of Gaussian kernel from standard deviation sigma.
DoG2D - class volume.DoG2D.
This is a 2D Difference of Gaussian convolution kernel.
DoG2D(double) - Constructor for class volume.DoG2D
 
DoG3D - class volume.DoG3D.
This is a 3D Difference of Gaussian convolution kernel.
DoG3D(double) - Constructor for class volume.DoG3D
 
doPerspective - Variable in class VolumeJ.VJRenderer
 
doPixeltracing - Variable in class VolumeJ.VJRenderer
Pixel tracing variables.
doPsi() - Method in class of3d.OF3DUserInterface
 
drotg_j(double[]) - Static method in class bijnum.Blas
This method constructs a Givens plane rotation.
dS(float[], int, int, int) - Static method in class volume.Diffusion
 
dS(HyperVolume, int, int, int, int) - Static method in class volume.Diffusion3D
 
dS(VolumeFloat, int, int, int) - Static method in class volume.Diffusion3D
 
dscal_j(int, double, double[], int) - Static method in class bijnum.Blas
This method scales a vector by a constant.
dscalp_j(int, double, double[], int) - Static method in class bijnum.Blas
This method scales a portion of a vector by a constant.
dsvdc_j(double[][], int, int, double[], double[], double[][], double[][], double[], int) - Static method in class bijnum.SVDC
This method decomposes a n by p matrix X into a product UDV´ where ...
dswap_j(int, double[], int, double[], int) - Static method in class bijnum.Blas
This method interchanges two vectors.
dt - Variable in class FlowJ.FlowJLucas
 
dU(HyperVolume, int, int, int, int) - Static method in class volume.Diffusion3D
 
dU(VolumeFloat, int, int, int) - Static method in class volume.Diffusion3D
 
dW(float[], int, int, int) - Static method in class volume.Diffusion
 
dW(HyperVolume, int, int, int, int) - Static method in class volume.Diffusion3D
 
dW(VolumeFloat, int, int, int) - Static method in class volume.Diffusion3D
 
dx - Variable in class FlowJ.FlowJLucas
 
dx - Variable in class VolumeJ.VJVoxelLoc
Difference between ix/iy/iz and x/y/z [0-1].
dx(int, int, int, Kernel1D) - Method in class volume.VolumeFloat
 
dy - Variable in class FlowJ.FlowJLucas
 
dy - Variable in class VolumeJ.VJVoxelLoc
 
dy(int, int, int, Kernel1D) - Method in class volume.VolumeFloat
 
dz - Variable in class VolumeJ.VJVoxelLoc
 
dz(int, int, int, Kernel1D) - Method in class volume.VolumeFloat
 

E

e1 - Static variable in class FlowJ.FlowJSpotNoise
 
e12 - Static variable in class FlowJ.FlowJSpotNoise
 
e1d - Static variable in class FlowJ.FlowJSpotNoise
 
e2 - Static variable in class FlowJ.FlowJSpotNoise
 
e22 - Static variable in class FlowJ.FlowJSpotNoise
 
e2d - Static variable in class FlowJ.FlowJSpotNoise
 
edge - Variable in class volume.Volume
 
effectDragging(int, int) - Method in class VolumeJ.VJViewerCanvas
User pressed mouse button, moved mouse, and released.
eigenimages - Variable in class bijnum.BIJpca
The matrix of eigenimages, i.e.
eigenvalues - Variable in class bijnum.Jacobi
Deprecated.  
eigenvalues - Variable in class bijnum.BIJpca
The eigenvalues of the transpose of the covariance matrix.
eigenvalues - Variable in class bijnum.BIJJacobi
 
eigenvectors - Variable in class bijnum.Jacobi
Deprecated.  
eigenvectors - Variable in class bijnum.BIJpca
The eigenvectors of the transpose of the covariance matrix.
eigenvectors - Variable in class bijnum.BIJJacobi
 
endx - Variable in class of3d.OF3DDeformer
 
endy - Variable in class of3d.OF3DDeformer
 
endz - Variable in class of3d.OF3DDeformer
 
Equalize - class volume.Equalize.
Plugin containing methods to equalize imageas and volumes.
Equalize() - Constructor for class volume.Equalize
 
erf(double) - Static method in class bijnum.BIJstats
Compute the erf of x.
error(String) - Static method in class FlowJ.FlowJUserInterface
 
error(String) - Static method in class VolumeJ.VJUserInterface
Writes a string to an error channel.
extract(float[], int, int, int, int, int) - Static method in class volume.Transformer
Extract a new float [] image from an image.

F

fhtps(int, int, float[], float[]) - Method in class bijnum.BIJfht
Calculate the Power Spectrum of one row from 2D Hartley Transform.
file - Variable in class io.FileAndString
 
FileAndString - class io.FileAndString.
Utility class for OpenPreviewDialog
FileAndString(File, String) - Constructor for class io.FileAndString
 
filter - Variable in class io.OpenPreviewDialog
 
filterAll(ImageStack, int, float) - Method in class FlowJ.FlowJSingh
 
filterAll(ImageStack, int, float, float) - Method in class FlowJ.FlowJUras
 
filterAll(ImageStack, int, float, float) - Method in class FlowJ.FlowJFleet
 
filterAll(ImageStack, int, float, float, int) - Method in class FlowJ.FlowJLucas
Do filtering.
FINETHRESHOLD - Static variable in class VolumeJ.VJViewerCanvas
 
firstFrame(ImageStack, float, int) - Static method in class FlowJ.FlowJLucas
Return the first frame for which you can compute the flow.
fit(byte[], int) - Static method in class bijnum.BIJutil
Fit a byte image into a new power of 2 size image of newwidth * newwidth.
fit(float[], int) - Static method in class bijnum.BIJutil
Fit a float image into a new power of 2 size image of newwidth * newwidth.
fit(float[], int, int) - Static method in class bijnum.BIJutil
Fit a square image into a smaller image widthxheight, with the center in the center of the new image.
flatten(float[][]) - Static method in class bijnum.BIJmatrix
Deprecated.  
flipquad(float[]) - Method in class bijnum.BIJfht
Flip quadrants 1 and 3 and quadrants 2 and 4 of an image column vector.
floatvalue - Variable in class VolumeJ.VJValue
 
flow - Variable in class FlowJ.FlowJMapper
 
flow - Variable in class FlowJ.FlowJError
 
flow - Variable in class of3d.FlowJValue
 
Flow3JColorNoiseMapper - class FlowJ.Flow3JColorNoiseMapper.
This class maps a flow field in color spotnoise field.
Flow3JColorNoiseMapper(ImageProcessor, float[][][], int, int, int, float, float, float) - Constructor for class FlowJ.Flow3JColorNoiseMapper
 
Flow3JDynamicColorMapper - class FlowJ.Flow3JDynamicColorMapper.
This class maps dynamic color of a flow field.
Flow3JDynamicColorMapper(ImageProcessor, float[][][], int, int, int, float, float, float) - Constructor for class FlowJ.Flow3JDynamicColorMapper
 
FlowJ - package FlowJ
 
FlowJCanvas - class FlowJ.FlowJCanvas.
 
FlowJCanvas(ImagePlus) - Constructor for class FlowJ.FlowJCanvas
 
FlowJColorNoiseMapper - class FlowJ.FlowJColorNoiseMapper.
This class maps a flow field in colored spotnoise format.
FlowJColorNoiseMapper(ImageProcessor, float[][][], int, int, int, float, float, float) - Constructor for class FlowJ.FlowJColorNoiseMapper
 
FlowJDisplay - class FlowJ.FlowJDisplay.
OFDisplay class implements the 2D display of 2D flow fields in different formats.
FlowJDisplay() - Constructor for class FlowJ.FlowJDisplay
 
FlowJDynamicColor - class FlowJ.FlowJDynamicColor.
This is a class that implements 2D and 3D Dynamic Color Mapping.
FlowJDynamicColor() - Constructor for class FlowJ.FlowJDynamicColor
 
FlowJDynamicColorMapper - class FlowJ.FlowJDynamicColorMapper.
 
FlowJDynamicColorMapper(ImageProcessor, float[][][], int, int, int, float, float, float) - Constructor for class FlowJ.FlowJDynamicColorMapper
 
FlowJError - class FlowJ.FlowJError.
 
FlowJError(int, int) - Constructor for class FlowJ.FlowJError
 
FlowJException - exception FlowJ.FlowJException.
 
FlowJException() - Constructor for class FlowJ.FlowJException
 
FlowJException(int) - Constructor for class FlowJ.FlowJException
 
FlowJException(String) - Constructor for class FlowJ.FlowJException
 
FlowJFleet - class FlowJ.FlowJFleet.
 
FlowJFleet() - Constructor for class FlowJ.FlowJFleet
 
FlowJFlow - class FlowJ.FlowJFlow.
This class implements 2D flow fields and methods (including reading and writing and utility methods).
FlowJFlow() - Constructor for class FlowJ.FlowJFlow
 
FlowJFlow(int, int) - Constructor for class FlowJ.FlowJFlow
 
FlowJLucas - class FlowJ.FlowJLucas.
This is a class that implements the Lucas and Kanade optical flow algorithm.
FlowJLucas() - Constructor for class FlowJ.FlowJLucas
 
FlowJMapper - class FlowJ.FlowJMapper.
This class is the superclass for the OF display mappers.
FlowJMapper() - Constructor for class FlowJ.FlowJMapper
 
FlowJMapper(ImageProcessor, float[][][], int, int, int, float, float, float) - Constructor for class FlowJ.FlowJMapper
 
FlowJQuiverMapper - class FlowJ.FlowJQuiverMapper.
This class maps a quiver map of a flow field.
FlowJQuiverMapper(ImageProcessor, float[][][], int, int, int, float, float, float) - Constructor for class FlowJ.FlowJQuiverMapper
 
FlowJScintillansRender - class of3d.FlowJScintillansRender.
FlowJScintillansRender.
FlowJScintillansRender(VJInterpolator, VJShader, VJClassifier) - Constructor for class of3d.FlowJScintillansRender
 
FlowJSingh - class FlowJ.FlowJSingh.
 
FlowJSingh() - Constructor for class FlowJ.FlowJSingh
 
FlowJSpotNoise - class FlowJ.FlowJSpotNoise.
This class implements spot noise displaying of flow fields.
FlowJSpotNoise() - Constructor for class FlowJ.FlowJSpotNoise
 
FlowJSpotNoise(byte[], int, int, float) - Constructor for class FlowJ.FlowJSpotNoise
 
FlowJSpotNoise(int[], int, int, float) - Constructor for class FlowJ.FlowJSpotNoise
 
FlowJSpotNoiseMapper - class FlowJ.FlowJSpotNoiseMapper.
This class maps spotnoise of a flow field.
FlowJSpotNoiseMapper(ImageProcessor, float[][][], int, int, int, float, float, float) - Constructor for class FlowJ.FlowJSpotNoiseMapper
 
FlowJTrilinearVector - class of3d.FlowJTrilinearVector.
This class implements trilinear interpolation and interpolation of gradients for vector flow volumes.
FlowJTrilinearVector() - Constructor for class of3d.FlowJTrilinearVector
 
FlowJUras - class FlowJ.FlowJUras.
 
FlowJUras() - Constructor for class FlowJ.FlowJUras
 
FlowJUserInterface - class FlowJ.FlowJUserInterface.
This class links the FlowJ classes to the ImageJ interface.
Copyright (c) 1999-2003, Michael Abramoff.
FlowJUserInterface() - Constructor for class FlowJ.FlowJUserInterface
 
FlowJValue - class of3d.FlowJValue.
FlowJValue extends VJValue.
FlowJValue() - Constructor for class of3d.FlowJValue
 
FlowJValue(FlowJValue) - Constructor for class of3d.FlowJValue
 
FlowJValue(Object, float[]) - Constructor for class of3d.FlowJValue
 
FlowJValue(VJValue, float[]) - Constructor for class of3d.FlowJValue
 
FlowJValue(VJValue, float, float, float) - Constructor for class of3d.FlowJValue
 
fraction - Variable in class of3d.OFClassifierScintillans
 
fractionMagnitude - Variable in class VolumeJ.VJClassifierLevoy
 
full - Variable in class FlowJ.FlowJFlow
 
full(int, int) - Method in class FlowJ.FlowJFlow
 
function(double) - Method in class volume.Gaussian
Compute Difference of Gaussian (DoG) function at x symmetric around 0.
function(double) - Method in class volume.DoG
Compute Difference of Gaussian function at x.
function(double, double) - Method in class volume.Gaussian2D
Compute Gaussian function at x, y symmetric around 0,0.
function(double, double) - Method in class volume.DoG2D
Compute 2D Difference of Gaussian function (DoG) at x, y.
function(double, double) - Method in class volume.LoG
Compute Laplacian of Gaussian function at x,y.
function(double, double, double) - Method in class volume.Gaussian3D
Compute Gaussian function at x, y symmetric around 0,0.
function(double, double, double) - Method in class volume.DoG3D
Compute 3D Difference of Gaussian function (DoG) at x, y.

G

g - Variable in class VolumeJ.VJAlphaColor
 
g - Variable in class VolumeJ.VJrgbValue
 
G - Variable in class FlowJ.FlowJLucas
 
g(double, double) - Static method in class volume.Diffusion3D
 
g(float, float) - Static method in class volume.Diffusion
 
GaborCos - class volume.GaborCos.
This class implements a Gabor (even) cosine wave 1d convolution kernel for separated convolutions.
GaborCos(double, double) - Constructor for class volume.GaborCos
Create a Gabor cosine kernel of width sigma tuned to w.
GaborSin - class volume.GaborSin.
This class implements a Gabor (odd) sine wave 1d convolution kernel for separated convolutions.
GaborSin(double, double) - Constructor for class volume.GaborSin
Create a Gabor sine kernel of width sigma tuned to w.
gamma - Variable in class bijnum.BIJgifa
 
gammaln(double) - Static method in class bijnum.BIJfunctions
 
GaussElim(float[], float[]) - Static method in class bijnum.BIJmatrix
Gaussian elimination method with backward substitution to solve a system of linear equations.
Gaussian - class volume.Gaussian.
This is a 1D separated 0-th order Gaussian convolution kernel.
Gaussian() - Constructor for class volume.Gaussian
 
Gaussian(double) - Constructor for class volume.Gaussian
Create a Gaussian kernel from standard deviation sigma.
Gaussian(int) - Constructor for class volume.Gaussian
Deprecated.  
Gaussian2D - class volume.Gaussian2D.
This is a 2D separated 0 order Gaussian convolution kernel.
Gaussian2D() - Constructor for class volume.Gaussian2D
 
Gaussian2D(double) - Constructor for class volume.Gaussian2D
 
Gaussian3D - class volume.Gaussian3D.
This is a 3D separated 0 order Gaussian convolution kernel.
Gaussian3D() - Constructor for class volume.Gaussian3D
 
Gaussian3D(double) - Constructor for class volume.Gaussian3D
 
GAUSSIANDERIV - Static variable in class FlowJ.FlowJLucas
Types of derivative computation.
GaussianDerivative - class volume.GaussianDerivative.
This class implement a scale space Gaussian n-th order derivative 1d convolution kernel for separated convolutions.
GaussianDerivative(double) - Constructor for class volume.GaussianDerivative
Create a Gaussian first order derivative kernel for scale.
GaussianDerivative(double, int) - Constructor for class volume.GaussianDerivative
Create a Gaussian n'th order derivative kernel for scale.
gaussianEllipse(float, float, float, float) - Method in class FlowJ.FlowJSpotNoise
 
gcomposite - Static variable in class FlowJ.FlowJSpotNoise
 
ge - Static variable in class FlowJ.FlowJSpotNoise
 
get() - Method in class VolumeJ.VJValue
 
get() - Method in class VolumeJ.VJShade
 
get(int) - Method in class VolumeJ.VJShade
 
get(int, int) - Method in class FlowJ.FlowJFlow
 
get(int, int) - Method in class VolumeJ.VJZBuffer
Get a depth at i,j.
get(int, int, int) - Method in class VolumeJ.VJThresholdedVolume
Get the threshold value as a boolean.
get(int, int, int) - Method in class VolumeJ.VJBinaryShell
Get the shell value as a boolean.
get(int, int, int) - Method in class of3d.OF3DFlow
 
get(int, int, int) - Method in class volume.Volume
 
get(int, int, int) - Method in class volume.VolumeShort
Get the voxel value as a Number.
get(int, int, int) - Method in class volume.VolumeInteger
Fill the volume from stack s with depth slices from start.
get(int, int, int) - Method in class volume.VolumeRGB
Get the brightness of the voxel at x,y,z as an integer between 0-255.
get(int, int, int) - Method in class volume.VolumeFloat
Get the voxel value as a Number.
get(int, int, int) - Method in class volume.HyperVolume
Get the vector value of the hypervolume that is at x,y,z.
getA() - Method in class VolumeJ.VJPlane
Get the A for the plane equation Ax+By+C+D=0 of this plane
getAlpha() - Method in class VolumeJ.VJAlphaColor
 
getAlpha(int, int) - Method in class of3d.OF3DSpot
 
getAlphaDeg(int, int) - Method in class FlowJ.FlowJFlow
 
getAspectx() - Method in class volume.Volume
 
getAspecty() - Method in class volume.Volume
 
getAspectz() - Method in class volume.Volume
 
getAverageMag() - Method in class VolumeJ.VJGradient
 
getB() - Method in class VolumeJ.VJPlane
Get the B for the plane equation Ax+By+C+D=0 of this plane
getBackground() - Method in class VolumeJ.VJShader
 
getBackground() - Method in class VolumeJ.VJOutlineShader
 
getBins() - Method in class bijnum.BIJmi
 
getBlue() - Method in class VolumeJ.VJAlphaColor
 
getBuffer() - Method in class VolumeJ.VJZBuffer
 
getC() - Method in class VolumeJ.VJPlane
Get the D for the plane equation Ax+By+C+D=0 of this plane
getClass(int) - Static method in class VolumeJ.VJClassifiers
Return the class belonging to index i.
getClassifier() - Method in class VolumeJ.VJRenderer
 
getClassifier(int) - Static method in class VolumeJ.VJClassifiers
 
getColumn(int) - Method in class VolumeJ.VJMatrix
Return the n-th column of the 3D transform matrix as a vector.
getCoordinates() - Method in class bijnum.BIJpca
Get the eigenvector coordinate matrix an as a matrix.
getCoordinatesImage() - Method in class bijnum.BIJpca
Get the eigenvector coordinate matrix an as an image (a float []) of width x height = eigenvectors.length.
getD() - Method in class VolumeJ.VJPlane
Get the D for the plane equation Ax+By+C+D=0 of this plane
getDefaultWindowSize() - Static method in class volume.Equalize
 
getDepth() - Method in class volume.Volume
 
getDiffuse() - Method in class VolumeJ.VJLight
 
getDimensions() - Method in class VolumeJ.VJGradient
 
getDirectory() - Method in class io.OpenPreviewDialog
 
getEdge() - Method in class volume.Volume
Get the edge in the volume beyond which a voxel is not valid.
getEigenImage(int) - Method in class bijnum.BIJpca
Compute the normalized image for eigenimage j so that it can be displayed with the same gray-scale as all others.
getFile() - Method in class io.FileAndString
 
getFileNames() - Method in class io.OpenPreviewDialog
End events coming from dialogwindow.
getFloatField(TextField) - Method in class VolumeJ.VJUserInterface
Get the value of a Textfield as a float.
getFloatPixels(Object) - Static method in class bijnum.BIJutil
Convert the pixels in array into a float vector.
getGradient() - Method in class VolumeJ.VJPlane
Return the gradient of a plane (the normal vector) as a VJGradient.
getGreen() - Method in class VolumeJ.VJAlphaColor
 
getHeight() - Method in class FlowJ.FlowJUras
 
getHeight() - Method in class FlowJ.FlowJSingh
 
getHeight() - Method in class FlowJ.FlowJFlow
 
getHeight() - Method in class FlowJ.FlowJFleet
 
getHeight() - Method in class VolumeJ.VJProjection
Return the height of the images in sliceArray.
getHeight() - Method in class volume.Volume
 
getHue() - Method in class VolumeJ.VJValueHSB
 
getImageArray() - Method in class VolumeJ.VJProjection
Return the slice array this back projection is based on.
getImageStack() - Method in class VolumeJ.VJBinaryShell
Make an ImageJ imagestack from this shell.
getImageStack() - Method in class volume.VolumeRGB
Make an ImageJ imagestack from the brightness info.
getImageStack() - Method in class volume.VolumeFloat
 
getImageWindows() - Method in class VolumeJ.VJUserInterface
Get the ids of all open windows that are ImageJ stacks.
getImageWindows() - Method in class VolumeJ.VJSurfaceJ
Get the ids of all open windows that are suitable for this plugin.
getIndex() - Method in class VolumeJ.VJValue
 
getIndexed() - Method in class volume.VolumeShort
 
getInterpolator() - Method in class VolumeJ.VJRenderer
 
getIntField(TextField) - Method in class VolumeJ.VJUserInterface
Get the value of a Textfield as an int.
getIntValue() - Method in class VolumeJ.VJValue
 
getJointHistogram() - Method in class bijnum.BIJmi
 
getLength() - Method in class volume.HyperVolume
 
getLight() - Method in class VolumeJ.VJShader
Get the Light, if any.
getLongField(TextField) - Method in class VolumeJ.VJUserInterface
Get a long from a TextField.
getLUT(VJClassifier, String) - Method in class VolumeJ.VJUserInterface
Set the LUT of a classifier from an ImageJ or NIH LUT file.
getLUT(VJClassifier, String) - Method in class VolumeJ.VJSurfaceJ
Set the LUT of a classifier from an ImageJ or NIH LUT file.
getmag() - Method in class VolumeJ.VJGradient
 
getmag(int) - Method in class VolumeJ.VJGradient
 
getMagnitude(int, int) - Method in class FlowJ.FlowJFlow
 
getMask(Roi, int, int) - Static method in class bijnum.BIJutil
Make a mask within an image widthxheight for Roi.
getMatrixWidth(ImagePlus) - Static method in class bijnum.BIJutil
Compute the width of the images in imp, or the ROI if one has been selected.
getMatrixWidth(ImagePlus, double) - Static method in class bijnum.BIJutil
Compute the width of the images in imp, containing a stack, including scaling.
getMax(float[][], int) - Static method in class VolumeJ.VJMatrix
Find the homogenuous coordinate with the highest value in an array of coordinates.
getMin(float[][], int) - Static method in class VolumeJ.VJMatrix
Find the homogenuous coordinate with the lowest value on a dimension in an array of coordinates.
getNames() - Static method in class VolumeJ.VJClassifiers
Return an array with the names of all VJClassifier classes.
getNiceScale(float, float) - Static method in class bijnum.BIJmi
Get a nice scale leading to a bin size of 128.
getnnx() - Method in class VolumeJ.VJVoxelLoc
Get the x-position rounded to the nearest int for nearest neighborhood interpolation.
getnny() - Method in class VolumeJ.VJVoxelLoc
Get the y-position rounded to the nearest int for nearest neighborhood interpolation.
getnnz() - Method in class VolumeJ.VJVoxelLoc
Get the z-position rounded to the nearest int for nearest neighborhood interpolation.
getOversamplingRatio() - Method in class VolumeJ.VJMatrix
Return the oversampling ratio for this (usually inverse) transformation matrix.
getPixels() - Method in class VolumeJ.VJRenderer
Get the viewport pixel buffer.
getPowerSpectrum(float[]) - Method in class bijnum.BIJfht
Get the power spectrum of the hartley transform (maxN x maxN pixels) and return as a byte array.
getProcessor() - Method in class volume.Diffusion
 
getRed() - Method in class VolumeJ.VJAlphaColor
 
getSaturation() - Method in class VolumeJ.VJValueHSB
 
getScale() - Method in class bijnum.BIJmi
Get the current scale.
getSecondaryClassifier() - Method in class VolumeJ.VJClassifier
 
getShader() - Method in class VolumeJ.VJRenderer
 
getShearCoefficients() - Method in class VolumeJ.VJMatrix
Return the shear coefficients as defined in Lacroute's thesis.
getSigma() - Method in class volume.Gaussian3D
 
getSigma() - Method in class volume.Gaussian
 
getSigma() - Method in class volume.Gaussian2D
 
getSigma() - Method in class volume.LoG
 
getSliceOrder(double, double) - Method in class VolumeJ.VJMatrix
Return the slice order as defined in Lacroutes thesis.
getSpecular() - Method in class VolumeJ.VJLight
 
getStepperColumn() - Method in class VolumeJ.VJMatrix
Return the third column of the 3D transform matrix as a vector.
getString() - Method in class io.FileAndString
 
getSupport(float, int) - Static method in class FlowJ.FlowJLucas
Return the number of frames needed for specific sigmat and gradient type.
getThreshold() - Method in class VolumeJ.VJClassifier
Get the classifier threshold.
getThreshold() - Method in class VolumeJ.VJClassifierInteger
 
getThreshold() - Method in class VolumeJ.VJClassifierIsosurface
 
getThreshold() - Method in class VolumeJ.VJClassifierLevoy
 
getThreshold() - Method in class of3d.OFClassifier
 
getTimePerPixel() - Method in class VolumeJ.VJRenderer
 
getTitle(int, float, float) - Method in class FlowJ.FlowJFlow
 
getTotalVariance() - Method in class bijnum.BIJpca
 
getTransformation() - Method in class VolumeJ.VJRenderer
 
getTree(String) - Method in class io.OpenPreviewDialog
Build a sequence of File's representing the full path of the path String up to root, and also include the roots both before and after path.
getType(Object[]) - Method in class VolumeJ.VJProjection
Return the datatype of the array components.
getValue() - Method in class VolumeJ.VJAlphaColor
 
getValue(int, int) - Method in class of3d.OF3DSpot
 
getVector(VJVoxelLoc) - Method in class of3d.OF3DDeformation
 
getViewingVector() - Method in class VolumeJ.VJMatrix
Return the viewing vector as defined in Lacroute's thesis.
getViewport() - Method in class VolumeJ.VJRenderer
Get the size of the viewport.
getViewportHeight() - Method in class VolumeJ.VJRenderer
Get the height of the viewport.
getViewportWidth() - Method in class VolumeJ.VJRenderer
Get the width of the viewport.
getVolume() - Method in class VolumeJ.VJRenderer
Get the volume in this renderer.
getVolume() - Method in class volume.VolumeInteger
 
getVolume() - Method in class volume.VolumeFloat
 
getWeights() - Method in class VolumeJ.VJVoxelLoc
 
getWidth() - Method in class FlowJ.FlowJUras
 
getWidth() - Method in class FlowJ.FlowJSingh
 
getWidth() - Method in class FlowJ.FlowJFlow
 
getWidth() - Method in class FlowJ.FlowJFleet
 
getWidth() - Method in class VolumeJ.VJProjection
Return the width of the images in sliceArray.
getWidth() - Method in class volume.Volume
 
getWindowNames(int[]) - Method in class VolumeJ.VJUserInterface
Get the names (by getTitle() method) from a list of windows.
getx() - Method in class VolumeJ.VJGradient
 
getx() - Method in class VolumeJ.VJLight
 
getx() - Method in class VolumeJ.VJVoxelLoc
Get the x-position.
getx(int) - Method in class VolumeJ.VJGradient
 
getX(int, int) - Method in class FlowJ.FlowJFlow
 
gety() - Method in class VolumeJ.VJGradient
 
gety() - Method in class VolumeJ.VJLight
 
gety() - Method in class VolumeJ.VJVoxelLoc
Get the y-position.
gety(int) - Method in class VolumeJ.VJGradient
 
getY(int, int) - Method in class FlowJ.FlowJFlow
 
getz() - Method in class VolumeJ.VJGradient
 
getz() - Method in class VolumeJ.VJLight
 
getz() - Method in class VolumeJ.VJVoxelLoc
Get the z-position.
getz(int) - Method in class VolumeJ.VJGradient
 
gp - Static variable in class FlowJ.FlowJSpotNoise
 
gradient(byte[], int, int, VJVoxelLoc) - Static method in class VolumeJ.VJTrilinear
Interpolate the gradient *xyz* in a byte volume.
gradient(byte[], int, int, VJVoxelLoc) - Static method in class VolumeJ.VJNearestNeighbor
Interpolate the gradient *xyz* in a byte volume.
gradient(double[]) - Method in class VolumeJ.VJShape
 
gradient(float[][][], VJVoxelLoc) - Static method in class VolumeJ.VJTrilinear
Interpolate the gradient *xyz* in a float volume.
gradient(float[][][], VJVoxelLoc) - Static method in class VolumeJ.VJNearestNeighbor
Interpolate the gradient *xyz* in a float volume (central difference).
gradient(OF3DFlow, VJVoxelLoc) - Method in class of3d.FlowJTrilinearVector
Compute an interpolated gradient from a flow vector volume.
gradient(short[][][], int, VJVoxelLoc) - Static method in class VolumeJ.VJTrilinear
Interpolate the gradient *xyz* in a short volume with a mask.
gradient(short[][][], VJVoxelLoc) - Static method in class VolumeJ.VJTrilinear
Interpolate the gradient *xyz* in a short volume.
gradient(short[][][], VJVoxelLoc) - Static method in class VolumeJ.VJNearestNeighbor
Interpolate the gradient *xyz* in a short volume (central difference).
gradient(Volume, VJVoxelLoc) - Method in class VolumeJ.VJInterpolator
Interpolate the gradient of v at location vl.
gradient(Volume, VJVoxelLoc) - Method in class VolumeJ.VJTrilinear
Compute an interpolated gradient from a volume.
gradient(Volume, VJVoxelLoc) - Method in class VolumeJ.VJNearestNeighbor
Compute an interpolated gradient from a volume.
gradientChoice - Variable in class VolumeJ.VJUserInterface
 
GRADIENTCT - Static variable in class VolumeJ.VJClassifiers
 
gradientKernel - Variable in class FlowJ.FlowJLucas
 
gradients() - Method in class FlowJ.FlowJUras
 
GRAYBYTE - Static variable in class VolumeJ.VJRenderer
Defines type of image the rendering is output to: grayscale.
GRAYSCALE - Static variable in class VolumeJ.VJClassifier
Classifier can return a RGB VJAlphaColor.
gScaleSpace(double, double) - Static method in class volume.Diffusion3D
 
gScaleSpace(float, float) - Static method in class volume.Diffusion
 

H

halfwidth - Variable in class volume.Kernel
 
hasLUT() - Method in class VolumeJ.VJClassifier
Return whether or not this classifier supports a user loadable LUT.
hasLUT() - Method in class VolumeJ.VJClassifierIsosurface
Tell renderer that this classifier does not have a LUT.
hasLUT() - Method in class VolumeJ.VJClassifierLevoy
Tell renderer that this classifier has user settable LUT.
hasLUT() - Method in class of3d.OFClassifierScintillans
Does not support user loadable LUTs.
hasWeights - Variable in class VolumeJ.VJVoxelLoc
 
height - Variable in class VolumeJ.VJReconstructor
 
height - Variable in class VolumeJ.VJRenderer
Boundaries of viewspace volume (the viewport) in k,j,i space.
height - Variable in class of3d.OF3DDeformer
 
height - Variable in class volume.Volume
Dimensions of the volume.
Hessian - class volume.Hessian.
This class implements computing the Hessian tensor matrix of an image, and computing the determinant (to detect blobs) and largest eigenvalues (to detect edges).
Hessian() - Constructor for class volume.Hessian
 
histogram(float[], float, float, int) - Static method in class bijnum.BIJstats
Compute a histogram with n bins for the vector v, each bin separated by d.
hsb - Variable in class VolumeJ.VJValueHSB
 
hue(float[], float) - Static method in class FlowJ.FlowJDynamicColor
Transform the 2D orientation of a vector into a hue (in float rgb format [0-1.0]).
hv - Variable in class volume.HyperVolume
 
hv - Variable in class volume.Diffusion3D
 
HyperVolume - class volume.HyperVolume.
This is a class that implements a float hyper (4D) volumes and operations including convolutions on it.
HyperVolume() - Constructor for class volume.HyperVolume
Creates the null hypervolume.
HyperVolume(ImageStack, int) - Constructor for class volume.HyperVolume
Create a new hypervolume from a stack of volumes.
HyperVolume(ImageStack, int, int, int, Kernel1D) - Constructor for class volume.HyperVolume
Creates a hypervolume depthxn from a stack containing n volumes of depth depth and convolve around center with a filtering kernel on the fly.
HyperVolume(int, int, int, int) - Constructor for class volume.HyperVolume
Creates a hypervolume with width, height, depth, length

I

i - Static variable in class FlowJ.FlowJSpotNoise
 
iList - Variable in class VolumeJ.VJUserInterface
 
imageStackFromMatrix(float[][], int) - Static method in class bijnum.BIJutil
Create an ImageJ ImageStack out of a float matrix.
imageStackFromMatrix(short[][], int) - Static method in class bijnum.BIJutil
Create an ImageJ ImageStack out of a float matrix.
imagesVolumeToSurfaceVolume(VolumeShort, int, float, float, float, float) - Static method in class VolumeJ.VJSurfacePlotShell
Convert the k'th 2-D image slice in vimages to a surface VolumeShort.
imp - Variable in class VolumeJ.VJRenderViewInteractive
 
imp - Variable in class volume.Diffusion
 
impr - Variable in class FlowJ.FlowJMapper
 
in(double, double, double) - Method in class volume.Volume
Check whether x,y,z are within the edges.
includeNormals - Variable in class FlowJ.FlowJLucas
 
index - Static variable in class FlowJ.FlowJSpotNoise
 
index - Variable in class VolumeJ.VJValue
 
index - Variable in class volume.VolumeRGB
The index value for each voxel, if any.
indexChoice - Variable in class VolumeJ.VJUserInterface
 
indexOfCurrentDir - Variable in class io.OpenPreviewDialog
Holds the index in the list of "directory".
info - Variable in class FlowJ.FlowJException
 
info - Variable in class bijnum.BIJException
 
info - Variable in class bijnum.SVDCException
 
initClassifiers() - Static method in class VolumeJ.VJClassifiers
 
initClassifiers() - Static method in class of3d.OF3DClassifiers
 
initializing - Variable in class VolumeJ.VJUserInterface
 
insert(double, int, int) - Method in class VolumeJ.VJZBuffer
Insert a depth at i,j into the z-buffer.
inserts - Static variable in class bijnum.BIJknn
 
instance - Static variable in class VolumeJ.VJUserInterface
This window.
interpolationChoice - Variable in class VolumeJ.VJUserInterface
 
interpolator - Variable in class VolumeJ.VJRenderer
Voxel interpolator.
intersect(int, int, int) - Method in class VolumeJ.VJCell
 
intersectRay(float, float) - Method in class VolumeJ.VJPlane
Optimization for finding intersection of this plane with a ray running through x0, y0, 0 with derivative 0,0,1.
intersectTracing(int, int, int) - Method in class VolumeJ.VJCell
 
intoStack(ImageStack) - Method in class volume.VolumeFloat
 
intoStack(ImageStack) - Method in class volume.HyperVolume
Transfer hv into stack is.
intoStack(ImageStack) - Method in class volume.Diffusion3D
 
intToHSB(float[], int) - Static method in class volume.VolumeRGB
Utility routine to convert an ARGB int format to float [] HSB format.
intvalue - Variable in class VolumeJ.VJValue
 
inverse() - Method in class VolumeJ.VJMatrix
Invert this matrix.
inverse(float[][]) - Static method in class bijnum.BIJmatrix
Invert a symmetric matrix m.
io - package io
 
ioffset - Variable in class VolumeJ.VJReconstructor
 
ioffset - Variable in class VolumeJ.VJRenderer
Start of rays in viewspace.
ioffset - Variable in class of3d.OF3DDeformer
 
isamax_j(int, double[], int) - Static method in class bijnum.Blas
This method finds the index of the element of a vector that has the maximum absolute value.
isGrayscale() - Method in class VolumeJ.VJAlphaColor
 
isIndexed() - Method in class volume.VolumeRGB
 
ISOSURFACE - Static variable in class VolumeJ.VJUserInterface
 
ISOSURFACE - Static variable in class VolumeJ.VJClassifiers
 
isStatic() - Method in class of3d.OFClassifier
 
isStatic() - Method in class of3d.OFClassifierScintillans
 
isValid(VJVoxelLoc, Volume) - Method in class VolumeJ.VJInterpolator
Does vl fall within the bounds of volume for a specific interpolation kernel?
isValid(VJVoxelLoc, Volume) - Method in class VolumeJ.VJTrilinear
Does vl fall within the bounds of a volume for interpolation?
isValid(VJVoxelLoc, Volume) - Method in class VolumeJ.VJNearestNeighbor
Does vl fall within the bounds of volume for a nearest neighbor interpolation?
isValidGradient(VJCell, Volume) - Method in class VolumeJ.VJInterpolator
Does cell c fall within the bounds of a volume for nearest neighbor gradient interpolation?
isValidGradient(VJCell, Volume) - Method in class VolumeJ.VJTrilinear
Does cell c fall within the bounds of a volume for nearest neighbor gradient interpolation? Bounds are -2...+3 of the cell location (translates to -2...+2 for the voxel location).
isValidGradient(VJCell, Volume) - Method in class VolumeJ.VJNearestNeighbor
Does cell c fall within the bounds of a volume for nearest neighbor gradient interpolation?
isValidGradient(VJVoxelLoc, Volume) - Method in class VolumeJ.VJInterpolator
Does vl fall within the bounds of volume for nearest neighbor gradient interpolation?
isValidGradient(VJVoxelLoc, Volume) - Method in class VolumeJ.VJTrilinear
Does vl fall within the bounds of a volume for trilinear gradient interpolation?
isValidGradient(VJVoxelLoc, Volume) - Method in class VolumeJ.VJNearestNeighbor
Does vl fall within the bounds of volume for nearest neighbor gradient interpolation?
itemStateChanged(ItemEvent) - Method in class VolumeJ.VJUserInterface
React to action e.
itemStateChanged(ItemEvent) - Method in class io.OpenPreviewDialog
 
iterations - Static variable in class volume.Diffusion
 
iterations - Static variable in class volume.Diffusion3D
 
ix - Variable in class VolumeJ.VJCell
Position of this cell in objectspace coordinates.
ix - Variable in class VolumeJ.VJVoxelLoc
integer floor of voxel location.
iy - Variable in class VolumeJ.VJCell
Position of this cell in objectspace coordinates.
iy - Variable in class VolumeJ.VJVoxelLoc
 
iz - Variable in class VolumeJ.VJCell
Position of this cell in objectspace coordinates.
iz - Variable in class VolumeJ.VJVoxelLoc
 

J

j - Static variable in class FlowJ.FlowJSpotNoise
 
Jacobi - class bijnum.Jacobi.
Deprecated.  
Jacobi(int) - Constructor for class bijnum.Jacobi
Deprecated. Create the eigenvectors and eigenvalues that will be computed.
jinc - Variable in class VolumeJ.VJCell
 
joffset - Variable in class VolumeJ.VJReconstructor
 
joffset - Variable in class VolumeJ.VJRenderer
Start of rays in viewspace.
joffset - Variable in class of3d.OF3DDeformer
 

K

k - Variable in class VolumeJ.VJValue
 
k - Variable in class bijnum.BIJgifa
 
k - Variable in class volume.Kernel1D
 
k - Variable in class volume.Kernel3D
 
k - Variable in class volume.Kernel2D
 
k - Variable in class volume.Kernel4D
 
k - Static variable in class volume.Diffusion
 
k - Static variable in class volume.Diffusion3D
 
kDistances - Variable in class bijnum.BIJknn
Some variables that I do not want to allocate for every element.
Kernel - class volume.Kernel.
This class is the generic type for all 1D, 2D and 3D kernels.
Kernel() - Constructor for class volume.Kernel
 
Kernel1D - class volume.Kernel1D.
This class is the generic type for all 1D kernels.
Kernel1D() - Constructor for class volume.Kernel1D
 
Kernel2D - class volume.Kernel2D.
This class is the generic type for all 2D kernels.
Kernel2D() - Constructor for class volume.Kernel2D
 
Kernel3D - class volume.Kernel3D.
This class is the generic type for all 3D kernels.
Kernel3D() - Constructor for class volume.Kernel3D
 
Kernel4D - class volume.Kernel4D.
This class is the generic type for all 4D kernels.
Kernel4D() - Constructor for class volume.Kernel4D
 
kernelToString() - Method in class volume.Kernel
 
kernelToString() - Method in class volume.Kernel1D
 
kernelToString() - Method in class volume.Kernel3D
 
kernelToString() - Method in class volume.Kernel2D
 
keyPressed(KeyEvent) - Method in class VolumeJ.VJUserInterface
 
keyReleased(KeyEvent) - Method in class VolumeJ.VJUserInterface
 
keyTyped(KeyEvent) - Method in class VolumeJ.VJUserInterface
React to action e.
kill() - Method in class VolumeJ.VJRenderView
Stops the shell.
kill() - Method in class VolumeJ.VJRenderer
The kill method is called when this renderer is to stop.
kinc - Variable in class VolumeJ.VJCell
 
kIndices - Variable in class bijnum.BIJknn
 
koffset - Variable in class VolumeJ.VJReconstructor
 
koffset - Variable in class VolumeJ.VJRenderer
Start of rays in viewspace.
koffset - Variable in class of3d.OF3DDeformer
 

L

lambda - Static variable in class volume.Diffusion
 
lambda - Static variable in class volume.Diffusion3D
 
largest(float[], float[], int, double) - Static method in class volume.Hessian
Compute the largest Hessian eigenvectors of a 2-D image.
largest(float[], int, double) - Static method in class volume.Hessian
Compute the largest Hessian eigenvectors of a 2-D image.
lastFrame(ImageStack, float, int) - Static method in class FlowJ.FlowJLucas
Return the last frame for which you can compute the flow.
length - Variable in class volume.HyperVolume
 
LEVOY - Static variable in class VolumeJ.VJClassifiers
 
LEVOYDEPTHCUEING - Static variable in class VolumeJ.VJClassifiers
 
LEVOYINDEXNE0 - Static variable in class VolumeJ.VJClassifiers
 
LEVOYNOINDEX - Static variable in class VolumeJ.VJClassifiers
 
light - Variable in class VolumeJ.VJShader
A light (position in viewspace coordinates).
lightField - Variable in class VolumeJ.VJUserInterface
 
lightx - Static variable in class VolumeJ.VJUserInterface
 
lighty - Static variable in class VolumeJ.VJUserInterface
 
lightz - Static variable in class VolumeJ.VJUserInterface
 
LINEAR - Static variable in class VolumeJ.VJClassifiers
 
list - Variable in class io.OpenPreviewDialog
 
ln(float[], float[]) - Static method in class bijnum.BIJmatrix
Compute the natural logarithmr of each element in vector v and put into r.
load(ImageProcessor, int) - Method in class volume.VolumeShort
Fill the volume with depth 1 with a single image ip.
load(ImageProcessor, int) - Method in class volume.VolumeInteger
 
load(ImageStack, int) - Method in class volume.VolumeShort
Fill this volume from stack s with from slice start.
load(ImageStack, int) - Method in class volume.VolumeInteger
 
load(ImageStack, int) - Method in class volume.VolumeFloat
 
load(Object[], int) - Method in class volume.VolumeRGB
Fill the brightness volume b with the int[] slices, starting at slice start.
loadImage(int[][], byte[]) - Method in class volume.VolumeInteger
 
loadImage(int[][], int[]) - Method in class volume.VolumeInteger
 
loadImage(short[][], byte[]) - Method in class volume.VolumeShort
Load an image b into i.
loadImage(short[][], short[]) - Method in class volume.VolumeShort
Load an image sh into i.
loadInverse(ImageStack, int) - Method in class volume.VolumeShort
Inversely load a volume from the stack centered around center with the first one last.
loadInverse(ImageStack, int) - Method in class volume.VolumeInteger
 
loadInverse(ImageStack, int) - Method in class volume.VolumeFloat
 
loadSlice(int[][], ImageStack, int) - Method in class volume.VolumeInteger
 
loadSlice(short[][], ImageStack, int) - Method in class volume.VolumeShort
Load a slice io from stack s into image i.
LoG - class volume.LoG.
This is a 2D Laplacian of Gaussian convolution kernel.
LoG(double) - Constructor for class volume.LoG
Create a Laplacian of Gaussian kernel from standard deviation sigma.
log2(int) - Method in class bijnum.BIJfht
 
lostOwnership(Clipboard, Transferable) - Method in class FlowJ.FlowJUserInterface
 
lostOwnership(Clipboard, Transferable) - Method in class VolumeJ.VJUserInterface
 
lut - Variable in class VolumeJ.VJClassifierLevoy
 
lutChoice - Variable in class VolumeJ.VJUserInterface
 

M

m - Variable in class VolumeJ.VJRenderView
State variables.
m - Variable in class VolumeJ.VJRenderer
Transformation matrix and inverse.
magConvolutionxy(float[], int, int, Kernel1D) - Static method in class volume.Convolver
Deprecated.  
magConvolutionxy(float[], int, int, Kernel2D) - Static method in class volume.Convolver
Deprecated.  
magnitude - Static variable in class FlowJ.FlowJSpotNoise
 
magnitude3D(float[]) - Static method in class FlowJ.FlowJFlow
Return the magnitude of a rectangular motion vector.
makeBitReverseTable(int) - Method in class bijnum.BIJfht
 
makeSinCosTables(int) - Method in class bijnum.BIJfht
 
map() - Method in class volume.VolumeFloat
 
map(byte[], float, float, float) - Static method in class FlowJ.FlowJDynamicColor
This method maps a polar 3d vector with orientations and speed (0-1) to a dynamic color in rgb.
map(ColorProcessor) - Method in class FlowJ.FlowJError
 
map(float[], int, int) - Method in class FlowJ.SSD
 
map(float, float, float) - Static method in class FlowJ.FlowJDynamicColor
 
map(Graphics, int, int, FlowJFlow, FlowJFlow) - Static method in class FlowJ.FlowJError
 
map2D(byte[], float, float) - Static method in class FlowJ.FlowJDynamicColor
This method maps a polar 2d vector with orientation and magnitude (0-1) to a dynamic color in rgb.
map3D(byte[], float, float, float) - Static method in class FlowJ.FlowJDynamicColor
Transform a polar 3D vector (orientationxy in the xy-plane, orientationz along the z axis and normalized magnitude (0-1)), to a dynamic color in rgb (0-255), with hue standing for orientationxy, intensity standing for orientationz and saturation standing for magnitude.
mapAverage(Graphics) - Method in class FlowJ.FlowJError
 
mapImage(float[][][], boolean[][], ImageProcessor, int, int, float, float, float) - Static method in class FlowJ.FlowJDisplay
Map the 2D flow field f into an imageprocessor ([vx, vy][y][x]).
mapImage(ImageProcessor, int, int, float, float) - Method in class FlowJ.FlowJFlow
 
mappingChoice - Variable in class VolumeJ.VJUserInterface
 
mask(float[], float[]) - Static method in class bijnum.BIJmatrix
Return a vector containing only the elements in v that have a mask value != 0.
maskIndex - Variable in class VolumeJ.VJClassifierLevoy
 
maskIntensity - Variable in class VolumeJ.VJClassifierLevoy
 
maskMagnitude - Variable in class VolumeJ.VJClassifierLevoy
 
matmat_j(double[][], double[][], double[][], int, int, int) - Static method in class bijnum.Blas
This method multiplies an n x p matrix by a p x r matrix.
matrixFromImageStack(ImagePlus) - Static method in class bijnum.BIJutil
Convert the data in the ImageStack in imp into a float[][] matrix for further processing.
matrixFromImageStack(ImagePlus, double) - Static method in class bijnum.BIJutil
Convert the data in the ImageStack in imp into a float[][] matrix and scale by scaleFactor on the fly.
matrixFromImageStackRoi(ImagePlus) - Static method in class bijnum.BIJutil
Convert the data only within the rectangular Roi in the ImageStack in imp into a float[][] matrix for further processing.
mattran_j(double[][], double[][], int, int) - Static method in class bijnum.Blas
This method obtains the transpose of an n x p matrix.
matvec_j(double[][], double[], double[], int, int) - Static method in class bijnum.Blas
This method multiplies an n x p matrix by a p x 1 vector.
maxIntensity - Variable in class VolumeJ.VJClassifierLevoy
 
maxN - Variable in class bijnum.BIJfht
 
maxp - Variable in class FlowJ.FlowJMapper
 
maxp - Variable in class FlowJ.FlowJSpotNoise
 
maxq - Variable in class FlowJ.FlowJMapper
 
maxq - Variable in class FlowJ.FlowJSpotNoise
 
mean(float[][]) - Static method in class bijnum.BIJstats
 
mean(int, int[], float[], float[][], int, int) - Method in class FlowJ.SSD
 
mean(short[]) - Static method in class bijnum.BIJShortMatrix
 
meanColumn(float[][]) - Static method in class bijnum.BIJstats
 
meanColumnT(float[][]) - Static method in class bijnum.BIJstats
 
memoryInUse() - Method in class VolumeJ.VJRenderView
Compute memory usage for rendering.
message - Variable in class VolumeJ.VJRenderView
 
message - Variable in class VolumeJ.VJRenderer
 
mi - Variable in class VolumeJ.VJReconstructor
 
mi - Variable in class VolumeJ.VJRenderer
Transformation matrix and inverse.
mi - Variable in class of3d.OF3DDeformer
 
mi(float[], float[]) - Method in class bijnum.BIJmi
 
mi(short[], short[]) - Method in class bijnum.BIJmi
 
miLight - Variable in class VolumeJ.VJRenderer
Separate transformation matrix and inverse for the light.
min - Variable in class bijnum.BIJmi
 
min() - Method in class FlowJ.SSD
 
min(int, int, float[][], int[][]) - Method in class FlowJ.FlowJUras
 
minCond(int[][], float[][], int) - Method in class FlowJ.FlowJUras
 
minMagnitude - Static variable in class FlowJ.Flow3JColorNoiseMapper
 
minMagnitude - Static variable in class FlowJ.FlowJColorNoiseMapper
 
minMagnitude - Static variable in class FlowJ.FlowJSpotNoiseMapper
 
minmax() - Method in class VolumeJ.VJRenderer
Calculate the extents of the volume to be rendered in view and objectspace.
minmax(float[]) - Static method in class bijnum.BIJmatrix
 
minmax(float[][]) - Static method in class bijnum.BIJmatrix
 
minmax(short[]) - Static method in class bijnum.BIJShortMatrix
 
minmax(short[][]) - Static method in class bijnum.BIJShortMatrix
 
minmax(Volume, VJMatrix) - Static method in class VolumeJ.VJViewspaceUtil
Calculate minimum and maximum extents in xyz viewspace coordinates of volume v.
minmaxNot0(float[]) - Static method in class bijnum.BIJmatrix
 
minmaxNot0(float[][]) - Static method in class bijnum.BIJmatrix
 
mLight - Variable in class VolumeJ.VJRenderView
State variables.
mLight - Variable in class VolumeJ.VJRenderer
Separate transformation matrix and inverse for the light.
montage(float[][], int, int) - Static method in class bijnum.BIJutil
Make a montage of all images in a, with columns images per row, so that the width of the returned image will be awidth*columns.
mouseIsDown - Variable in class VolumeJ.VJViewerCanvas
 
mouseMoved(MouseEvent) - Method in class FlowJ.FlowJCanvas
 
mousePressed(MouseEvent) - Method in class FlowJ.FlowJCanvas
 
mousePressed(MouseEvent) - Method in class VolumeJ.VJViewerCanvas
Process a mouse button down event.
mouseReleased(MouseEvent) - Method in class FlowJ.FlowJCanvas
 
mouseReleased(MouseEvent) - Method in class VolumeJ.VJViewerCanvas
Process a mouse button up event.
move(float[]) - Method in class VolumeJ.VJVoxelLoc
Move the location of this voxel with delta's in dos.
move(float, float, float) - Method in class VolumeJ.VJCell
 
mse(float[], float[]) - Static method in class bijnum.BIJstats
Compute Mean Square Error (or residual) of vectors a and b.
mul(double) - Method in class volume.VolumeFloat
 
mul(double) - Method in class volume.HyperVolume
Multiply all voxels in this hypervolume by a constant.
mul(float[]) - Method in class VolumeJ.VJMatrix
Multiply a vector v with this transformation matrix and return the result as a vector.
mul(float[][], float[]) - Static method in class bijnum.BIJmatrix
Compute the outer product of a matrix and a vector v
mul(float[][], float[][]) - Static method in class bijnum.BIJmatrix
Compute the matrix product of m and n.
mul(float[][], float[][], boolean) - Static method in class bijnum.BIJmatrix
Compute the matrix product of m and n.
mul(float[][], float[][], float) - Static method in class bijnum.BIJmatrix
Multiply each element in matrix m by a scalar and put result in r.
mul(float[][], float[][], float[][], boolean) - Static method in class bijnum.BIJmatrix
Compute the matrix product of m and n into r.
mul(float[], float) - Static method in class bijnum.BIJmatrix
Deprecated.  
mul(float[], float[][], float[]) - Static method in class bijnum.BIJmatrix
Compute the outer product of a matrix and a vector v and put the result in r.
mul(HyperVolume, HyperVolume) - Method in class volume.HyperVolume
Multiply all voxels in this hypervolume by the voxels in b (NOT the inner product).
mul(VJMatrix) - Method in class VolumeJ.VJMatrix
Multiply this transformation matrix with another transformation matrix in place.
mul(VolumeFloat) - Method in class volume.VolumeFloat
 
mul(VolumeFloat, VolumeFloat) - Method in class volume.VolumeFloat
 
mulElements(double[], double[], double) - Static method in class bijnum.BIJmatrix
Multiply each element in v by a scalar and put in r.
mulElements(double[], double[], double[]) - Static method in class bijnum.BIJmatrix
Multiply all elements in vector a by elements in b and put in r.
mulElements(float[], float[]) - Static method in class bijnum.BIJmatrix
Multiply all elements in vector a by elements in b.
mulElements(float[], float[], double) - Static method in class bijnum.BIJmatrix
Multiply each element in v by a scalar and put in r.
mulElements(float[], float[], float[]) - Static method in class bijnum.BIJmatrix
Multiply all elements in vector a by elements in b and put in r.
mulOuter(float[], float[]) - Static method in class bijnum.BIJmatrix
Compute outer product of vector a and b.
mulT(float[][], float[][], boolean) - Static method in class bijnum.BIJmatrix
Compute the transpose of the outer product of the tranpose of a with b.

N

n - Variable in class VolumeJ.VJProjection
The number of projection images.
n - Variable in class VolumeJ.VJRenderViewCine
Total number of view to be rendered (in a stack)
n - Variable in class bijnum.BIJknn
The numbe rof different classes in classset.
n - Variable in class bijnum.BIJmi
 
n - Variable in class bijnum.BIJJacobi
 
n() - Method in class VolumeJ.VJProjection
Return the number of projection images in this projection.
n(float[]) - Static method in class bijnum.BIJstats
 
n(float[], float[]) - Static method in class bijnum.BIJstats
 
names - Variable in class io.OpenPreviewDialog
The names of the files that were selected, null if no selection.
newMatrix(int) - Static method in class bijnum.BIJtransform
Create a new (diagonal) transformation matrix for the number of dimensions.
newVector(float, float, float) - Static method in class VolumeJ.VJMatrix
Create a new 3-D homogenuous vector from 3 coordinates.
newView() - Method in class VolumeJ.VJRenderViewInteractive
Renders a view.
newViewportBuffer() - Method in class VolumeJ.VJRenderer
 
nextView(int) - Method in class VolumeJ.VJRenderViewCine
Prepare for the next rendering in a cine rendering.
nextView(int) - Method in class VolumeJ.VJSurfacePlotShell
Prepare for the (k+1) th rendering in a cine rendering.
no - Variable in class VolumeJ.VJOutlineShader
The outline exponent.
nonlinear(float[], double) - Static method in class volume.Convolver
Deprecated.  
norm(float[]) - Static method in class bijnum.BIJmatrix
Return length or norm of vector v.
normalize() - Method in class VolumeJ.VJGradient
 
normalize() - Method in class of3d.OF3DFlow
 
normalize(float[], double) - Static method in class volume.Convolver
Deprecated.  
normals(float, float) - Method in class FlowJ.FlowJFleet
 
notOpaque() - Method in class VolumeJ.VJAlphaColor
 
nrIndexBits - Variable in class VolumeJ.VJClassifierLevoy
 
nrIntensityBits - Variable in class VolumeJ.VJClassifierLevoy
 
nrMagnitudeBits - Variable in class VolumeJ.VJClassifierLevoy
 
nrot - Variable in class bijnum.BIJJacobi
 
nrot() - Method in class bijnum.Jacobi
Deprecated.  
nrot() - Method in class bijnum.BIJJacobi
 
number - Static variable in class VolumeJ.VJUserInterface
 

O

objectify(VJMatrix) - Method in class VolumeJ.VJLight
Transform the position of this light into another coordinate system.
of3d - package of3d
 
OF3DClassifiers - class of3d.OF3DClassifiers.
This class is a class whose only purpose is to contain all OFClassifier class definitions.
OF3DClassifiers() - Constructor for class of3d.OF3DClassifiers
 
OF3DDeformation - class of3d.OF3DDeformation.
 
OF3DDeformation() - Constructor for class of3d.OF3DDeformation
 
OF3DDeformation(float[]) - Constructor for class of3d.OF3DDeformation
 
OF3DDeformation(float, float, float, float, float, float, float) - Constructor for class of3d.OF3DDeformation
 
OF3DDeformer - class of3d.OF3DDeformer.
OF3DDeformer does a progressive deformation on a single volume, and creates a series of volumes that contain the progressively deformed volume.
OF3DDeformer() - Constructor for class of3d.OF3DDeformer
 
OF3DDisplay - class of3d.OF3DDisplay.
OF3DDisplay is an extension of OFDisplay to implement the 2D display of 3D flow fields.
OF3DDisplay() - Constructor for class of3d.OF3DDisplay
 
OF3DFlow - class of3d.OF3DFlow.
This class implements a volume consisting of 3D optical flows and methods useful for volume rendering.
OF3DFlow() - Constructor for class of3d.OF3DFlow
 
OF3DFlow(int, int, int) - Constructor for class of3d.OF3DFlow
 
OF3DFlow(int, int, int, float, float, float) - Constructor for class of3d.OF3DFlow
 
OF3DFlow(String) - Constructor for class of3d.OF3DFlow
 
OF3DHalfSpot - class of3d.OF3DHalfSpot.
This class implements the creation of 3D half oriented spots from a 3D vector.
OF3DHalfSpot() - Constructor for class of3d.OF3DHalfSpot
 
OF3DLucas - class of3d.OF3DLucas.
 
OF3DLucas(OF3DFlow, ImageStack, int, int, float, float, boolean) - Constructor for class of3d.OF3DLucas
 
OF3DSpot - class of3d.OF3DSpot.
This class implements the creation of 3D spots from a 3D vector.
OF3DSpot() - Constructor for class of3d.OF3DSpot
 
OF3DSpot(float[], float, float) - Constructor for class of3d.OF3DSpot
 
OF3DUserInterface - class of3d.OF3DUserInterface.
This class links the OF3D classes to the VJ classes and the ImageJ interface.
Copyright (c) 1999-2003, Michael Abramoff.
OF3DUserInterface() - Constructor for class of3d.OF3DUserInterface
 
OFClassifier - class of3d.OFClassifier.
This class is the superclass for all 3D optical flow visualization classifiers by extending VJClassifier.
OFClassifier() - Constructor for class of3d.OFClassifier
 
OFClassifierDCM2DNoGradient - class of3d.OFClassifierDCM2DNoGradient.
This class implements dynamic color mapping, a 2D classification function of 3D optical flows, displaying iso-shear surfaces.
OFClassifierDCM2DNoGradient() - Constructor for class of3d.OFClassifierDCM2DNoGradient
 
OFClassifierDCM3DNoGradient - class of3d.OFClassifierDCM3DNoGradient.
This class implements a classification function of 3D optical flows that sets the color of a voxel to the 3D DCM color of the corresponding 3D flow vector.
OFClassifierDCM3DNoGradient() - Constructor for class of3d.OFClassifierDCM3DNoGradient
 
OFClassifierScintillans - class of3d.OFClassifierScintillans.
This class implements a classification function of 3D optical flows that sets a scintillation corresponding in size, color and direction to the flow vector.
OFClassifierScintillans() - Constructor for class of3d.OFClassifierScintillans
 
OFClassifierScintillansIx255 - class of3d.OFClassifierScintillansIx255.
This class implements a classification function of 3D optical flows that sets a scintillation corresponding in size, color and direction to the flow vector.
OFClassifierScintillansIx255() - Constructor for class of3d.OFClassifierScintillansIx255
 
OFClassifierScintillansIxLT0 - class of3d.OFClassifierScintillansIxLT0.
This class implements a classification function of 3D optical flows that sets a scintillation corresponding in size, color and direction to the flow vector.
OFClassifierScintillansIxLT0() - Constructor for class of3d.OFClassifierScintillansIxLT0
 
OFClassifierScintillansNoFlow - class of3d.OFClassifierScintillansNoFlow.
This class implements a classification function of 3D optical flows that sets a scintillation corresponding in size, color and direction to the flow vector.
OFClassifierScintillansNoFlow() - Constructor for class of3d.OFClassifierScintillansNoFlow
 
OFClassifierScintillansNoStatic - class of3d.OFClassifierScintillansNoStatic.
This class implements a classification function of 3D optical flows that sets a scintillation corresponding in size, color and direction to the flow vector.
OFClassifierScintillansNoStatic() - Constructor for class of3d.OFClassifierScintillansNoStatic
 
OFXYZ - Static variable in class of3d.OF3DUserInterface
 
OFXZY - Static variable in class of3d.OF3DUserInterface
 
OFYZX - Static variable in class of3d.OF3DUserInterface
 
onTrace(int, int) - Method in class VolumeJ.VJRenderer
 
opacityCompute(double, double) - Method in class VolumeJ.VJClassifierLinear
Simple ramp classification function Overloads same function in VJClassifierLevoy.
opacityCompute(double, double, double, double) - Method in class VolumeJ.VJClassifierValue
Compute opacity from intensity only.
opacityCompute(float, float, float, float) - Method in class VolumeJ.VJClassifierLevoy
Implements Levoy's gradient tent function for precomputation.
opacityTable - Variable in class VolumeJ.VJClassifierLevoy
 
open - Variable in class io.OpenPreviewDialog
 
Open_Different_Sizes_As_Stack - class io.Open_Different_Sizes_As_Stack.
Opens images of different sizes as a stack.
Open_Different_Sizes_As_Stack() - Constructor for class io.Open_Different_Sizes_As_Stack
 
Open_HP_volume - class io.Open_HP_volume.
Opens a HP volume file as a stack.
Open_HP_volume() - Constructor for class io.Open_HP_volume
 
Open_Sequence_As_Stack - class io.Open_Sequence_As_Stack.
Opens a subset of a directory as a stack.
Open_Sequence_As_Stack() - Constructor for class io.Open_Sequence_As_Stack
 
OpenPreviewDialog - class io.OpenPreviewDialog.
Convenient file open dialog that can show header info (any you want, just extend this class).
OpenPreviewDialog(String, Object, String) - Constructor for class io.OpenPreviewDialog
Open a preview open dialog, a dialog that shows a list of files in the directory, and shows a text (currently header text) related to that file, to ease selection.
order - Variable in class volume.GaussianDerivative
 
orientationxy(float[]) - Static method in class FlowJ.FlowJFlow
 
orientationxy(float, float) - Static method in class FlowJ.FlowJFlow
return the orientation (in radians) in the xy plane of a rectangular motion vector r
orientationz(float[]) - Static method in class FlowJ.FlowJFlow
 
osv - Static variable in class VolumeJ.VJViewspaceRender
 
outputType - Variable in class VolumeJ.VJRenderer
Type of image output by this renderer: GRAYBYTE or COLORINT.
overThreshold(float) - Method in class VolumeJ.VJClassifierIsosurface
 

P

p - Static variable in class FlowJ.FlowJSpotNoise
 
panel - Variable in class io.OpenPreviewDialog
 
params() - Method in class volume.Diffusion
 
params(ImagePlus, VolumeFloat) - Method in class volume.Diffusion3D
 
params4D(ImagePlus) - Method in class volume.Diffusion3D
 
peak(int, int) - Method in class FlowJ.SSD
 
peakloc - Variable in class FlowJ.SSD
 
perform(AWTEvent) - Method in class VolumeJ.VJUserInterface
React to Event e.
perform(AWTEvent) - Method in class VolumeJ.VJSurfaceJ
React to Event e.
perform(AWTEvent) - Method in class of3d.OF3DUserInterface
React to Event e.
permutation(int) - Method in class VolumeJ.VJMatrix
Make a permutation for one of the major axes (x,y,z) Used for shear-warp rendering.
phi - Variable in class bijnum.BIJgifa
 
pixel(int, int, int, int, float, float) - Method in class FlowJ.FlowJMapper
 
pixel(int, int, int, int, float, float) - Method in class FlowJ.Flow3JColorNoiseMapper
 
pixel(int, int, int, int, float, float) - Method in class FlowJ.FlowJQuiverMapper
 
pixel(int, int, int, int, float, float) - Method in class FlowJ.FlowJColorNoiseMapper
 
pixel(int, int, int, int, float, float) - Method in class FlowJ.FlowJSpotNoiseMapper
 
pixel(int, int, int, int, float, float) - Method in class FlowJ.FlowJDynamicColorMapper
 
pixel(int, int, int, int, float, float) - Method in class FlowJ.Flow3JDynamicColorMapper
 
pixelms - Variable in class VolumeJ.VJRenderer
Amount of ms per pixel spent in rendering loop.
pixels - Variable in class FlowJ.FlowJMapper
 
pixels - Variable in class VolumeJ.VJRenderer
Image buffer, is a flat array of int's or byte's, dependent on outputType.
PIXELSDEGREES - Static variable in class VolumeJ.VJViewerCanvas
Mouse motion (in pixels) that stands for a single radian in rotation.
pixelSize - Variable in class VolumeJ.VJViewspaceRender
size of entry viewspacePixel.
polar(float[]) - Static method in class FlowJ.FlowJFlow
Convert a rectangular vector r to a vector in polar coordinates p.
polar(float[], float[]) - Static method in class FlowJ.FlowJFlow
 
polar(float[], float, float) - Static method in class FlowJ.FlowJFlow
 
polar(float, float) - Static method in class FlowJ.FlowJFlow
 
polar3D(float[], float[]) - Static method in class FlowJ.FlowJFlow
 
polar3D(float[], float, float, float) - Static method in class FlowJ.FlowJFlow
 
pow(double[], double[], double) - Static method in class bijnum.BIJmatrix
Compute the power'th power of each element in vector v and put into r.
pow(float[][], float) - Static method in class bijnum.BIJmatrix
Compute the power'th power of each entry in the matrix m.
pow(float[], double) - Static method in class volume.Convolver
Deprecated.  
pow(float[], float[], double) - Static method in class bijnum.BIJmatrix
Compute the power'th power of each element in vector v and put into r.
pow(float[], float[], float) - Static method in class bijnum.BIJmatrix
Compute the power'th power of each element in vector v and put into r.
prepare(float, float, int) - Method in class of3d.OF3DLucas
 
progress(double) - Method in class bijnum.BIJfht
Can be used to show progress in other programs.
progress(float) - Static method in class VolumeJ.VJUserInterface
Writes a progress bar to a status channel.
propagateClassifier() - Method in class VolumeJ.VJUserInterface
Propagate the change of classifier onto other dialog items and instances.
pScaling - Variable in class FlowJ.FlowJMapper
 
pseudoinverse(double[][], double[][], double) - Static method in class bijnum.BIJmatrix
Deprecated.  
pseudoinverse(float[][], float[][], double) - Static method in class bijnum.BIJmatrix
Deprecated.  
psi(int, int) - Method in class FlowJ.FlowJError
 
psiErr(float[], float[]) - Static method in class of3d.OF3DFlow
 
Pu - Variable in class bijnum.BIJmi
 
Pulleys - package Pulleys
 
Puv - Variable in class bijnum.BIJmi
 
Pv - Variable in class bijnum.BIJmi
 

Q

q - Static variable in class FlowJ.FlowJSpotNoise
 
qScaling - Variable in class FlowJ.FlowJMapper
 
quick(float[], int, int, int) - Static method in class volume.Transformer
Quickly transform an image for whole pixel shifts.
QUIVER - Static variable in class FlowJ.FlowJDisplay
 
quiver(FlowJFlow, float, float) - Static method in class FlowJ.FlowJDisplay
 

R

r - Variable in class VolumeJ.VJAlphaColor
 
r - Variable in class VolumeJ.VJrgbValue
 
random - Variable in class of3d.FlowJValue
 
randomFraction(float[], double) - Static method in class bijnum.BIJstats
Randomly sample a fraction of the elements of vector v.
RAYTRACE - Static variable in class VolumeJ.VJUserInterface
 
rc2DFHT(float[], boolean, int) - Method in class bijnum.BIJfht
Row-column Fast Hartley Transform
rcomposite - Static variable in class FlowJ.FlowJSpotNoise
 
read(String) - Method in class FlowJ.FlowJFlow
Read a flow field defined in a file.
read(String) - Method in class of3d.OF3DFlow
 
recompute(float) - Method in class FlowJ.SSD
 
Reconstructors - package Reconstructors
 
REG_AVERAGE - Variable in class FlowJ.FlowJLucas
 
REG_GAUSSIAN - Variable in class FlowJ.FlowJLucas
 
REG_GAUSSIAN_1D - Variable in class FlowJ.FlowJLucas
Types of regularization (smoothness constraint) computation.
render - Variable in class VolumeJ.VJUserInterface
 
renderCine - Variable in class VolumeJ.VJUserInterface
 
renderer - Variable in class VolumeJ.VJRenderView
The renderer
renderer - Variable in class VolumeJ.VJUserInterface
 
renderExtra - Variable in class VolumeJ.VJUserInterface
 
renderStereo - Variable in class VolumeJ.VJUserInterface
 
renderStop - Variable in class VolumeJ.VJUserInterface
 
renderSurfaceplot - Variable in class VolumeJ.VJSurfaceJ
 
renderToImageProcessor() - Method in class VolumeJ.VJRenderView
Render in a separate thread and make an image processor out of the resulting image.
renderToPixelArray() - Method in class VolumeJ.VJRenderView
Render in a separate thread and return the pixels with the rendering.
renderView - Variable in class VolumeJ.VJViewerCanvas
The rendering viewer
repmat(float[][], int, int) - Static method in class bijnum.BIJmatrix
repmat replicates a matrix in tiled form.
repmat(float[], int, int) - Static method in class bijnum.BIJmatrix
repmat replicates a vector in tiled form.
report(long) - Method in class VolumeJ.VJRenderView
 
resetClassifier() - Method in class of3d.OF3DUserInterface
Create and setup a classifier for the new threshold and width settings.
resetClassifier(int, int) - Method in class VolumeJ.VJUserInterface
Create and setup a classifier according to the classifier number index (index only vali within VJUserInterface).
resetClassifier(int, int) - Method in class VolumeJ.VJSurfaceJ
Create and setup a classifier according to the classifier number index (index only valid within VJUserInterface).
resetRenderer(VJInterpolator, VJClassifier, VJShader, int) - Method in class of3d.OF3DUserInterface
Create a renderer for the shader, interpolator and renderer.
resetRenderer(VJInterpolator, VJClassifier, VJShader, int, boolean, int, int, int, boolean, int, int) - Method in class VolumeJ.VJUserInterface
Create a renderer for the shader, interpolator and renderer.
resetShader(float, float, float, float, float, float) - Method in class VolumeJ.VJUserInterface
Create a shader and light for the current light coordinates and aspect ratio.
resetVolume(ImagePlus, ImagePlus, float, float, float) - Method in class VolumeJ.VJUserInterface
Change the volume to be rendered, based on the stack in window imp.
result - Variable in class volume.Diffusion
 
RGB - Static variable in class VolumeJ.VJClassifier
Classifier can return a RGB VJAlphaColor.
rho - Variable in class FlowJ.FlowJMapper
 
rho - Variable in class bijnum.BIJgifa
 
rho - Variable in class of3d.OFClassifierScintillans
 
rmse(float[], float[]) - Static method in class bijnum.BIJstats
Compute Root Mean Square Error of vectors a and b.
rotate(float[][], int, int, int, int, double, double) - Method in class bijnum.BIJJacobi
Rotate, used to be a macro in C sources.
rotateInPlane(float, float) - Method in class VolumeJ.VJRenderViewInteractive
Rotate the transformation matrix by viewing plane rotation angles rotx, roty.
rotatex(double) - Method in class VolumeJ.VJMatrix
Rotate the coordinate system around the x axis.
rotatex(float[][], double) - Static method in class bijnum.BIJtransform
Rotate a transformation matrix around the x-axis.
rotatey(double) - Method in class VolumeJ.VJMatrix
Rotate the coordinate system around the y axis.
rotatey(float[][], double) - Static method in class bijnum.BIJtransform
Rotate a transformation matrix around the y axis.
rotatez(double) - Method in class VolumeJ.VJMatrix
Rotate the coordinate system around the z axis.
rotatez(float[][], double) - Static method in class bijnum.BIJtransform
Rotate a transformation matrix around the z axis.
rotField - Variable in class VolumeJ.VJUserInterface
 
rotx - Variable in class VolumeJ.VJRenderView
State variables.
roty - Variable in class VolumeJ.VJRenderView
State variables.
rotz - Variable in class VolumeJ.VJRenderView
State variables.
rp - Static variable in class FlowJ.FlowJSpotNoise
 
rs - Variable in class VolumeJ.VJUserInterface
 
run() - Method in class VolumeJ.VJRenderView
Overload to make functional.
run() - Method in class VolumeJ.VJRenderViewSingle
The top level rendering thread handler.
run() - Method in class VolumeJ.VJRenderViewCine
The top level rendering thread handler.
run() - Method in class VolumeJ.VJRenderer
To be overloaded, does nothing.
run() - Method in class VolumeJ.VJIsosurfaceRender
Variables are all inherited from VJRenderer
run() - Method in class VolumeJ.VJViewspaceRender
Viewspace rendering.
run() - Method in class VolumeJ.VJRenderViewStereo
 
run() - Method in class VolumeJ.VJRender
Objectspace rendering method.
run() - Method in class VolumeJ.VJRenderViewInteractive
Generates the first view and stays on.
run() - Method in class of3d.OF3DLucas
 
run(String) - Method in class io.Open_HP_volume
 
run(String) - Method in class io.Open_Different_Sizes_As_Stack
 
run(String) - Method in class io.Open_Sequence_As_Stack
 
running - Variable in class VolumeJ.VJRenderView
 
running - Variable in class VolumeJ.VJRenderer
Flag indicating whether this renderer is running.

S

s - Variable in class VolumeJ.VJCell
 
s - Variable in class VolumeJ.VJBinaryShell
 
S - Variable in class bijnum.BIJfht
 
saveAsObject(String) - Method in class of3d.OF3DFlow
 
saveAsText(float[], String) - Static method in class bijnum.BIJutil
Save vector v as a text file.
scale - Variable in class VolumeJ.VJRenderView
State variables.
scale - Static variable in class VolumeJ.VJUserInterface
 
scale - Variable in class bijnum.BIJmi
 
scale - Variable in class volume.GaussianDerivative
 
scale(double, double, double) - Method in class VolumeJ.VJMatrix
Scale the coordinate system by sx, sy, sz.
scale(float[][], double, double) - Static method in class bijnum.BIJtransform
Scale a 2-D transformation matrix by sx, sy.
scale(float[][], double, double, double) - Static method in class bijnum.BIJtransform
Scale a 3-D transformation matrix by sx, sy, sz.
scaleField - Variable in class VolumeJ.VJUserInterface
 
scaleSpaceContrast - Variable in class volume.Diffusion
 
scaleSpaceContrast - Variable in class volume.Diffusion3D
 
sderiv - Static variable in class FlowJ.FlowJLucas
 
sderiv - Static variable in class of3d.OF3DLucas
 
search(int[], float[], float[], int) - Method in class bijnum.BIJknn
Find the k-nearest neighbors of vector v (N dimensional) in dataset and put indices in kIndices, distances in kDistances.
secondaryClassifier - Variable in class VolumeJ.VJClassifier
Contains a secondary classifier if needed in alphacolor.
selectedFileNames() - Method in class io.OpenPreviewDialog
Get the filenames that were selected as an array of Strings.
sem(double, double, double, double, double) - Static method in class bijnum.BIJstats
Compute the combined standard error of the mean of the two standard errors stderr0 and stderr1 and corresponding averages avg0 and avg1.
sem(float[]) - Static method in class bijnum.BIJstats
sem(1) computes the standard error of the mean of the elements of v.
sem(float[], float[]) - Static method in class bijnum.BIJstats
sem(2) computes the standard error of the mean of the elements of v only where the mask value is not 0.
sensitivities(float[], float[], int) - Static method in class bijnum.BIJstats
Compute the sensitivities of a test of which the result is in exp and the ground truth in truth, for all classes n that occur in truth.
sensitivity(float[], float[], int) - Static method in class bijnum.BIJstats
Compute sensitivity of a test of which the result is in exp and the ground truth in truth, for class c.
sequenceNumber - Variable in class VolumeJ.VJRenderer
 
set(int, int, float, float) - Method in class FlowJ.FlowJFlow
 
set(int, int, float, float, boolean) - Method in class FlowJ.FlowJFlow
 
set(int, int, int, int) - Method in class volume.VolumeShort
Deprecated.  
set(Object, int, int, int) - Method in class VolumeJ.VJThresholdedVolume
Set the threshold value to a boolean value.
set(Object, int, int, int) - Method in class VolumeJ.VJBinaryShell
Set the shell value to a boolean value.
set(Object, int, int, int) - Method in class of3d.OF3DFlow
 
set(Object, int, int, int) - Method in class volume.Volume
Set the voxel at x,y,z to value.
set(Object, int, int, int) - Method in class volume.VolumeShort
Set the voxel value to a Number.
set(Object, int, int, int) - Method in class volume.VolumeInteger
 
set(Object, int, int, int) - Method in class volume.VolumeRGB
Set the brightness of the voxel at x,y,z as an integer between 0-255.
set(Object, int, int, int) - Method in class volume.VolumeFloat
Set the voxel value to a Number.
set(Object, int, int, int) - Method in class volume.HyperVolume
Set the vector value of the hypervolume that is at x,y,z to value.
setAlpha(float) - Method in class VolumeJ.VJAlphaColor
 
setAspects(double, double, double) - Method in class volume.Volume
Set the aspect ratio of this volume.
setAxes(int) - Method in class of3d.OFClassifier
 
setAxes(int) - Method in class of3d.OFClassifierScintillans
Set the axes of the scintillation color coding.
setBackface(boolean) - Method in class VolumeJ.VJShader
Set the shader backfacing on or off.
setCalibration(Calibration) - Method in class FlowJ.FlowJFlow
 
setClassifier(VJClassifier) - Method in class VolumeJ.VJRenderer
 
setCutout(VJCutout) - Method in class VolumeJ.VJRenderer
 
setD(float) - Method in class VolumeJ.VJPlane
Set the D for the plane equation Ax+By+C+D=0 of this plane
setDescription(String) - Method in class VolumeJ.VJRenderer
 
setDisplayed(Object) - Method in class FlowJ.FlowJCanvas
 
setEdge(int) - Method in class volume.Volume
Set the edges in the volume beyond which a voxel is not valid.
setFields(Label, Label, Label, Label) - Method in class FlowJ.FlowJCanvas
 
setFraction(float) - Method in class of3d.OFClassifier
 
setFraction(float) - Method in class of3d.OFClassifierScintillans
Set the fraction of the flows that are displayed as scintillations.
setHighBits(ImageStack) - Method in class volume.VolumeShort
Combine the values of s into the index byte (high 8 bits) of the voxel scalars of this volume.
setIndex(int) - Method in class VolumeJ.VJValue
 
setIndex(Object[]) - Method in class volume.VolumeRGB
Combine the values of s into the index array of this volume.
setIndexed(boolean) - Method in class volume.VolumeShort
 
setInterpolator(VJInterpolator) - Method in class VolumeJ.VJRenderer
 
setLUT(byte[], byte[], byte[]) - Method in class VolumeJ.VJClassifier
Set up a user-defined LUT.
setLUT(byte[], byte[], byte[]) - Method in class VolumeJ.VJClassifierLevoy
Set the LUT to a user-defined LUT.
setMessage(String) - Method in class VolumeJ.VJRenderer
Set the rendering message.
setOpaque() - Method in class VolumeJ.VJAlphaColor
 
setOutputColor() - Method in class VolumeJ.VJRenderer
Set the output to color.
setOutputGrayscale() - Method in class VolumeJ.VJRenderer
Set the output to color.
setPixel(int, int, int) - Method in class VolumeJ.VJRenderer
Put color into the pixel array at i,j.
setPixel(VJAlphaColor, int, int) - Method in class VolumeJ.VJRenderer
Put the pixel into the pixel array at i,j.
setRenderView(VJRenderViewInteractive) - Method in class VolumeJ.VJViewerCanvas
Set the VJRenderViewInteractive instance to process actions.
setRho(float) - Method in class of3d.OFClassifier
 
setRho(float) - Method in class of3d.OFClassifierScintillans
Set the rho of the DCM.
setRotationSteps(float, float, float) - Method in class VolumeJ.VJRenderViewCine
Set the rotation steps around the x,y and z axes (per cine step).
setSecondaryClassifier(VJClassifier) - Method in class VolumeJ.VJClassifier
Sets an alternative classifier.
setSequenceNumber(int) - Method in class VolumeJ.VJRenderer
 
setShader(VJShader) - Method in class VolumeJ.VJRenderer
The shader has changed.
setStaticVolume(Volume) - Method in class of3d.OF3DFlow
Sets a secondary static volume for which the flow has been computed.
setThreshold(float) - Method in class VolumeJ.VJClassifierIsosurface
 
setThreshold(float) - Method in class VolumeJ.VJClassifierLevoy
Set center of gradient tent function.
setTransformation(VJMatrix) - Method in class VolumeJ.VJRenderer
Set the transformation matrix of the renderer to m.
setTransformation(VJMatrix, VJMatrix) - Method in class VolumeJ.VJRenderer
Set the transformation matrix of the renderer to m and the special light transformation matrix to correct the light position (should not be influenced by e.g.
setup() - Method in class of3d.OFClassifierScintillans
 
setup(VJMatrix, VJMatrix) - Method in class VolumeJ.VJCutout
 
setup(Volume, VJMatrix) - Method in class VolumeJ.VJReconstructor
Setup the reconstructor for a specific viewport size width and height.
setup(Volume, VJMatrix) - Method in class of3d.OF3DDeformer
 
setupOpacities(float) - Method in class VolumeJ.VJClassifierLevoy
Compute the opacities for a range of voxel values and gradient values.
setViewport(int, int) - Method in class VolumeJ.VJRenderer
Set the viewport to a specific size.
setVolume(Volume) - Method in class VolumeJ.VJRenderer
The volume has changed.
setVolume(Volume) - Method in class VolumeJ.VJIsosurfaceRender
The volume has changed.
setWidth(float) - Method in class VolumeJ.VJClassifierLevoy
Set width of gradient tent function.
setx(int) - Method in class VolumeJ.VJVoxelLoc
Set the value for x.
sety(int) - Method in class VolumeJ.VJVoxelLoc
Set the value for x.
setz(float) - Method in class VolumeJ.VJVoxelLoc
Set the value for z.
setz(int) - Method in class VolumeJ.VJVoxelLoc
Set the value for z.
sgradientKernel - Variable in class FlowJ.FlowJLucas
 
shade(VJGradient) - Method in class VolumeJ.VJShader
Empty shading method uses *normalized* gradient g.
shade(VJGradient) - Method in class VolumeJ.VJPhongShader
Shading method for Phong illumination model that uses normalized gradient g.
shade(VJGradient) - Method in class VolumeJ.VJOutlineShader
Outline shading method uses *normalized* gradient g.
shader - Variable in class VolumeJ.VJRenderer
Surface shader.
shader - Variable in class VolumeJ.VJUserInterface
 
shear(double, double) - Method in class VolumeJ.VJMatrix
Shear the coordinate system by sx, sy.
shortMatrixFromImageStack(ImagePlus) - Static method in class bijnum.BIJutil
Convert the data in the ImageStack in imp into a short [][] matrix for further processing.
show() - Method in class FlowJ.FlowJUserInterface
Shows Dialog.
showDialog() - Method in class VolumeJ.VJUserInterface
Sets up the dialog window with all (dynamic) elements filled in.
showDialog() - Method in class VolumeJ.VJSurfaceJ
Sets up the dialog window with all (dynamic) elements filled in.
showDialog() - Method in class of3d.OF3DUserInterface
 
showDirs(Choice, String) - Method in class io.OpenPreviewDialog
Fill the choiceDir with all directory names up to the current directory and all roots.
showFileHeader(File) - Method in class io.OpenPreviewDialog
 
showFiles(List, String, Object) - Method in class io.OpenPreviewDialog
Fill the list with all files from the directory that fit filter.
showProgress(float) - Static method in class FlowJ.FlowJUserInterface
 
showStatus(String) - Static method in class FlowJ.FlowJUserInterface
 
sigma - Static variable in class VolumeJ.VJSurfaceJ
 
sigma - Variable in class volume.Gaussian3D
 
sigma - Variable in class volume.Gaussian
 
sigma - Variable in class volume.Gaussian2D
 
SIGMA - Static variable in class FlowJ.FlowJSpotNoise
 
SIGMA3DM - Static variable in class of3d.OF3DSpot
 
sigmaEllipse(int) - Method in class FlowJ.FlowJSpotNoise
 
sigmaField - Variable in class VolumeJ.VJSurfaceJ
 
sigmah - Variable in class of3d.OF3DSpot
Relative short and long axis of the spot is determined by the two Gaussian prob distr standard deviations SIGMA and SIGMA3DM.
SIGMAH - Static variable in class of3d.OF3DSpot
 
sigmal2 - Static variable in class FlowJ.FlowJSpotNoise
 
SIGMAM - Static variable in class FlowJ.FlowJSpotNoise
 
sigmas - Variable in class FlowJ.FlowJSpotNoise
 
sigmas2 - Static variable in class FlowJ.FlowJSpotNoise
 
sign_j(double, double) - Static method in class bijnum.Blas
This method implements the FORTRAN sign (not sin) function.
singlechannel() - Method in class VolumeJ.VJShade
 
sKernel - Variable in class FlowJ.FlowJLucas
 
sliceArray - Variable in class VolumeJ.VJProjection
The projection images.
sliceArray - Variable in class volume.VolumeRGB
The slices for this volume with the actual RGB data.
sliceHeight - Variable in class VolumeJ.VJProjection
 
sliceWidth - Variable in class VolumeJ.VJProjection
The width of each projection image.
sliding(float[], int, float, int, boolean) - Static method in class volume.Equalize
Perform sliding window averaging on image.
smallest(float[], float[], int, double) - Static method in class volume.Hessian
Compute the smallest Hessian eigenvectors of a 2-D image.
smallest(float[], int, double) - Static method in class volume.Hessian
Compute the smallest Hessian eigenvectors of a 2-D image.
snr - Variable in class bijnum.BIJgifa
 
Sobel - class volume.Sobel.
This class implements a 2D separated Sobel differentiation kernel.
Sobel() - Constructor for class volume.Sobel
Initialize Sobel 2D kernel.
SOBEL2D - Static variable in class FlowJ.FlowJLucas
 
Sobel3D - class volume.Sobel3D.
This class implements a 3D Sobel differentiation kernel.
SOBEL3D - Static variable in class FlowJ.FlowJLucas
 
Sobel3D() - Constructor for class volume.Sobel3D
Initialize Sobel 1D kernel.
SOBEL3DT - Variable in class of3d.OF3DLucas
 
Sobel4D - class volume.Sobel4D.
This class implements a 4D Sobel differentiation kernel.
Sobel4D() - Constructor for class volume.Sobel4D
Initialize Sobel 1D kernel.
sort() - Method in class bijnum.Jacobi
Deprecated.  
sort() - Method in class bijnum.BIJJacobi
Sort the eigenvalues/eigenvectors on the basis of the eigenvalues, largest first.
sort(float[]) - Static method in class bijnum.BIJmatrix
Sort a vector, but return the result as a vector of indices, conserving the original vector.
sort(float[], float[], float[][]) - Static method in class bijnum.BIJmatrix
Sort a vector and a matrix simultaneously based on the order of items in a third vector.
sourceChoice - Variable in class VolumeJ.VJUserInterface
 
specificities(float[], float[], int) - Static method in class bijnum.BIJstats
Compute the specificities of a test of which the result is in exp and the ground truth in truth, for all classes n that occur in truth.
specificity(float[], float[], int) - Static method in class bijnum.BIJstats
Compute specificity of a test of which the result is in exp and the ground truth in truth, for class c.
spectrum(float[]) - Static method in class bijnum.BIJstats
Compute the spectrum of v.
specular - Variable in class VolumeJ.VJLight
 
spot(int, int, float, int, float[]) - Method in class FlowJ.FlowJSpotNoise
 
spot(int, int, float, int, int, int, float[]) - Method in class FlowJ.FlowJSpotNoise
 
SPOTNOISE - Static variable in class FlowJ.FlowJDisplay
 
sqrt() - Method in class volume.VolumeFloat
 
sregul - Static variable in class FlowJ.FlowJLucas
 
SSD - class FlowJ.SSD.
 
SSD(int, int) - Constructor for class FlowJ.SSD
 
SSD(VolumeFloat, int, int, int, int, int) - Constructor for class FlowJ.SSD
 
startMouseX - Variable in class VolumeJ.VJViewerCanvas
 
startMouseY - Variable in class VolumeJ.VJViewerCanvas
 
startx - Variable in class of3d.OF3DDeformer
 
starty - Variable in class of3d.OF3DDeformer
 
startz - Variable in class of3d.OF3DDeformer
 
staticPixel - Variable in class of3d.OFClassifierScintillans
 
status(String) - Static method in class VolumeJ.VJUserInterface
Writes a string to a status channel.
stdev(float[]) - Static method in class bijnum.BIJstats
Compute stdev (SQRT(var)) of all values in vector v.
stdev(float[], float[]) - Static method in class bijnum.BIJstats
stdev(2) computes the stddev of the elements of only where the mask value is not 0.
stepx - Variable in class VolumeJ.VJRenderViewCine
The rotation steps to go to the next view.
stepy - Variable in class VolumeJ.VJRenderViewCine
The rotation steps to go to the next view.
stepz - Variable in class VolumeJ.VJRenderViewCine
The rotation steps to go to the next view.
stereoDifference - Static variable in class VolumeJ.VJRenderViewStereo
 
string - Variable in class io.FileAndString
 
sub(float[][], float[][], float[]) - Static method in class bijnum.BIJmatrix
Subtract the elements of a vector v from each element of a matrix m, columnwise.
sub(float[][], float[][], float[][]) - Static method in class bijnum.BIJmatrix
Subtract a matrix n from a matrix m.
sub(float[], float[]) - Static method in class bijnum.BIJmatrix
 
sub(float[], float[], float) - Static method in class bijnum.BIJmatrix
 
sub(VolumeFloat) - Method in class volume.VolumeFloat
Subtract volume v1 from this volume.
subElements(float[], float[], float[]) - Static method in class bijnum.BIJmatrix
 
submean(float[][], int) - Method in class bijnum.BIJgifa
Computes the mean of the submatrices of a MxN matrix F.
subset(float[][], int[]) - Static method in class bijnum.BIJmatrix
Make a subset of m, include only those row vectors with an index which is in indices.
subset(float[][], int, int) - Static method in class bijnum.BIJmatrix
Make a subset of m, including only those with an index which is equal or larger than start up to and including last.
subset(float[], int) - Static method in class bijnum.BIJmatrix
Make a subset of v, including only those with an index which is equal or larger than start.
subset(float[], int[]) - Static method in class bijnum.BIJmatrix
Make a subset of v, including only those with an index which is in indices.
subset(float[], int, int) - Static method in class bijnum.BIJmatrix
Make a subset of v, including only those with an index which is equal or larger than start up to and including last.
subsetColumns(float[][], int[]) - Static method in class bijnum.BIJmatrix
Make a subset of m, including only those columns of the row vectors with an index which is in indices.
SUBTRACT - Static variable in class FlowJ.FlowJLucas
 
subtract(float[], float[]) - Static method in class volume.Convolver
Deprecated.  
subtractAverage() - Method in class of3d.OF3DFlow
 
suggestCineViewport(Volume, VJMatrix, float, float, float, int) - Static method in class VolumeJ.VJViewspaceUtil
Determine the optimal size for a cine rendering in coordinate system m of the whole v.
suggestViewport(Volume, VJMatrix) - Static method in class VolumeJ.VJViewspaceUtil
Determine the optimal size for the rendering in coordinate system m of the whole v.
sum(double[]) - Static method in class bijnum.BIJstats
Compute average of all values in vector v.
sum(float[]) - Static method in class bijnum.BIJstats
sum(1) computes average of all values in vector v.
sum(float[], float[]) - Static method in class bijnum.BIJstats
sum(2) computes the sum of the elements of vector v only where the mask value is not 0.
support - Variable in class FlowJ.FlowJLucas
 
support() - Method in class volume.Kernel
 
surface(int, int, int) - Method in class VolumeJ.VJBinaryShell
Determine whether cell contains a surface.
surface(VJCell) - Method in class VolumeJ.VJBinaryShell
Determine whether cell contains a surface.
surface(VJVoxelLoc) - Method in class VolumeJ.VJBinaryShell
Determine whether there is a surface in the cell that vl is in.
SVDC - class bijnum.SVDC.
This class contains the LINPACK DSVDC (singular value decomposition) routine.
SVDC() - Constructor for class bijnum.SVDC
 
SVDCException - exception bijnum.SVDCException.
This is the exception produced by the Singular Value Decomposition method.
SVDCException() - Constructor for class bijnum.SVDCException
 
SVDCException(int) - Constructor for class bijnum.SVDCException
 
SVDCException(String) - Constructor for class bijnum.SVDCException
 
sweeps - Variable in class bijnum.BIJJacobi
 
sweeps() - Method in class bijnum.Jacobi
Deprecated.  
sweeps() - Method in class bijnum.BIJJacobi
 

T

tau - Variable in class FlowJ.FlowJLucas
 
tempArr - Variable in class bijnum.BIJfht
 
test() - Static method in class bijnum.BIJmatrix
 
testCheckbox - Variable in class VolumeJ.VJUserInterface
 
textarea - Variable in class io.OpenPreviewDialog
 
tgradientKernel - Variable in class FlowJ.FlowJLucas
 
theta - Variable in class VolumeJ.VJProjection
Angle (in degrees) of each projection image.
threshold - Variable in class VolumeJ.VJClassifierIsosurface
 
threshold - Variable in class VolumeJ.VJClassifierLevoy
 
threshold - Static variable in class VolumeJ.VJUserInterface
 
thresholdField - Variable in class VolumeJ.VJUserInterface
 
thresholdFraction(float[], double) - Static method in class bijnum.BIJstats
 
thresholdFraction(float[], float) - Static method in class bijnum.BIJstats
Find the value in vector over which fraction of all values in vector lie.
tile(float[], int) - Static method in class bijnum.BIJutil
Fit an image into a new image of newwidth * newwidth, where newwidth is next large power of 2 than width.
tKernel - Variable in class FlowJ.FlowJLucas
 
tlb - Variable in class VolumeJ.VJVoxelLoc
 
tlf - Variable in class VolumeJ.VJVoxelLoc
trilinear interpolation weights.
toDisk - Variable in class VolumeJ.VJRenderViewCine
Whether the cine rendering will be written to disk only or also displayed.
toGrid(float[], float[]) - Static method in class FlowJ.FlowJFlow
Translate to grid coordinates.
toLongString() - Method in class VolumeJ.VJClassifier
This method can be overloaded as necessary
toLongString() - Method in class VolumeJ.VJClassifierIsosurface
 
toLongString() - Method in class VolumeJ.VJClassifierLevoy
 
toLongString() - Method in class VolumeJ.VJClassifierLNotIndex0
 
toLongString() - Method in class VolumeJ.VJClassifierGradientCT
 
toLongString() - Method in class VolumeJ.VJClassifierValue
 
toLongString() - Method in class VolumeJ.VJClassifierLevoyCueing
 
toLongString() - Method in class VolumeJ.VJLight
 
toLongString() - Method in class VolumeJ.VJClassifierLNoIndex
 
toLongString() - Method in class VolumeJ.VJClassifierRGB
 
toStack() - Method in class FlowJ.FlowJFlow
 
toStack() - Method in class volume.HyperVolume
Convert this hypervolume to a stack.
toStack(OF3DFlow, int, int, float, float) - Static method in class of3d.OF3DDisplay
 
toStack(OF3DFlow, int, int, float, VolumeFloat, float) - Static method in class of3d.OF3DDisplay
 
toString() - Method in class FlowJ.FlowJUras
 
toString() - Method in class FlowJ.FlowJSingh
 
toString() - Method in class FlowJ.FlowJLucas
 
toString() - Method in class FlowJ.FlowJFleet
 
toString() - Method in class FlowJ.SSD
 
toString() - Method in class FlowJ.FlowJException
 
toString() - Method in class VolumeJ.VJGradient
 
toString() - Method in class VolumeJ.VJClassifier
Return a String with information of this classifier.
toString() - Method in class VolumeJ.VJAlphaColor
 
toString() - Method in class VolumeJ.VJInterpolator
 
toString() - Method in class VolumeJ.VJShader
 
toString() - Method in class VolumeJ.VJPhongShader
 
toString() - Method in class VolumeJ.VJCell
 
toString() - Method in class VolumeJ.VJClassifierLevoy
Tell calling program name of this classifier.
toString() - Method in class VolumeJ.VJValue
 
toString() - Method in class VolumeJ.VJRenderView
 
toString() - Method in class VolumeJ.VJShade
 
toString() - Method in class VolumeJ.VJPlane
 
toString() - Method in class VolumeJ.VJClassifierLevoyCueing
 
toString() - Method in class VolumeJ.VJMatrix
 
toString() - Method in class VolumeJ.VJLight
 
toString() - Method in class VolumeJ.VJOutlineShader
 
toString() - Method in class VolumeJ.VJVoxelLoc
 
toString() - Method in class VolumeJ.VJTrilinear
 
toString() - Method in class VolumeJ.VJNearestNeighbor
 
toString() - Method in class bijnum.Jacobi
Deprecated.  
toString() - Method in class bijnum.BIJException
 
toString() - Method in class bijnum.BIJJacobi
 
toString() - Method in class of3d.OFClassifierScintillans
 
toString() - Method in class of3d.OFClassifierScintillansNoStatic
 
toString() - Method in class of3d.OFClassifierDCM3DNoGradient
 
toString() - Method in class of3d.OFClassifierScintillansIx255
 
toString() - Method in class of3d.FlowJValue
 
toString() - Method in class of3d.OFClassifierScintillansNoFlow
 
toString() - Method in class of3d.OFClassifierDCM2DNoGradient
 
toString() - Method in class of3d.OFClassifierScintillansIxLT0
 
toString() - Method in class of3d.OF3DLucas
 
toString() - Method in class volume.Kernel
 
toString() - Method in class volume.Volume
Return a string describing the volume.
toString() - Method in class volume.Gaussian3D
 
toString() - Method in class volume.Gaussian
 
toString() - Method in class volume.Sobel
 
toString() - Method in class volume.Kernel4D
 
toString() - Method in class volume.Sobel4D
 
toString() - Method in class volume.DoG3D
 
toString() - Method in class volume.Sobel3D
 
toString() - Method in class volume.Gaussian2D
 
toString() - Method in class volume.DoG2D
 
toString() - Method in class volume.HyperVolume
 
toString() - Method in class volume.DoG
 
toString() - Method in class volume.LoG
 
toString() - Method in class volume.GaussianDerivative
 
toString() - Method in class volume.CentralDiff
 
toString(double[]) - Static method in class bijnum.BIJutil
 
toString(double[][]) - Static method in class bijnum.BIJutil
 
toString(float[]) - Static method in class bijnum.BIJutil
 
toString(float[][]) - Static method in class bijnum.BIJutil
 
toString(int, float, float) - Static method in class FlowJ.FlowJDisplay
Convert FlowJDisplay parameters to a String.
toString(int, int, float, VolumeFloat, float) - Static method in class of3d.OF3DDisplay
 
toString(short[]) - Static method in class bijnum.BIJShortMatrix
 
toString(Volume) - Method in class VolumeJ.VJCell
Format a String of the contents of this cell, als include the volume values at the vertex of this cell.
toStringFaces() - Method in class VolumeJ.VJCell
Format a String from the equations of all faces in this cell.
toStringVertices(float[][]) - Method in class VolumeJ.VJCell
Format a String from the extents of this cell.
totalVariance - Variable in class bijnum.BIJpca
Total accumulative variance.
trace(int, int) - Method in class VolumeJ.VJRenderer
Start pixeltracing for the i,j pixel in the viewport.
trace(String) - Method in class VolumeJ.VJRenderer
 
trace(VJValue, VJGradient) - Method in class VolumeJ.VJClassifier
For debugging: print value, index and gradient.
trace(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierIsosurface
 
traceCheckbox - Variable in class VolumeJ.VJUserInterface
 
traceField - Variable in class VolumeJ.VJUserInterface
 
tracei - Variable in class VolumeJ.VJRenderer
 
tracej - Variable in class VolumeJ.VJRenderer
 
traceString - Variable in class VolumeJ.VJRenderer
 
traceWrite() - Method in class VolumeJ.VJRenderer
 
transform(float[], int, float[]) - Static method in class volume.Transformer
Transform image using the transformation parameters in p.
transform(float[], int, float[][]) - Static method in class volume.Transformer
Bilinearly transform an image using a 2-D transformation matrix m.
transform(float[], int, float[], float, float) - Static method in class volume.Transformer
Transform image using the transformation parameters in p.
transform(ImageProcessor, float[]) - Static method in class volume.Transformer
Transform the image in fp by translation parameters p
Transformer - class volume.Transformer.
This class implements static methods for transforming images and volumes.
Transformer() - Constructor for class volume.Transformer
 
transformVertices(VJMatrix, float[][]) - Static method in class VolumeJ.VJCell
Transform the vertex coordinates of a cell into a different coordinate system.
translate(double, double, double) - Method in class VolumeJ.VJMatrix
Translate the coordinate system to tx, ty, tz.
translate(float[][], double, double) - Static method in class bijnum.BIJtransform
Translate a 2-D transformation matrix by these values.
translate(float[][], double, double, double) - Static method in class bijnum.BIJtransform
Translate a 3-D transformation matrix by these values.
translateCubeTest(float, float, float) - Method in class of3d.OF3DFlow
 
translateTest(float, float, float) - Method in class of3d.OF3DFlow
 
transpose(float[][]) - Static method in class bijnum.BIJmatrix
Compute the transpose of a matrix m.
transposeR(float[], int) - Method in class bijnum.BIJfht
 
trb - Variable in class VolumeJ.VJVoxelLoc
 
trf - Variable in class VolumeJ.VJVoxelLoc
 
trueFlow - Variable in class FlowJ.FlowJError
 
trunc(float[][], int) - Static method in class bijnum.BIJmatrix
Truncate a matrix to a new column length n.
trunc(float[], int) - Static method in class bijnum.BIJmatrix
Truncate a vector to a new length n.
ttest(float[], float[]) - Static method in class bijnum.BIJstats
Perform Student's t-test on two data sets data1 and data2, with the the t values into t and the probabilities into prob.
tx - Variable in class VolumeJ.VJLight
 
ty - Variable in class VolumeJ.VJLight
 
type - Variable in class VolumeJ.VJProjection
 
tz - Variable in class VolumeJ.VJLight
 

U

UNDERFLOW_LIMIT - Static variable in class bijnum.BIJJacobi
 
unitvar(float[]) - Static method in class bijnum.BIJstats
Make a new vector of v that has zero mean and unit variance.
ux(int, int, Kernel2D) - Method in class volume.VolumeFloat
 
uy(int, int, Kernel2D) - Method in class volume.VolumeFloat
 

V

v - Variable in class FlowJ.FlowJFlow
 
v - Variable in class VolumeJ.VJThresholdedVolume
 
v - Variable in class VolumeJ.VJReconstructor
 
v - Variable in class VolumeJ.VJRenderer
Volume to be rendered (polymorphic).
v - Variable in class VolumeJ.VJBinaryShell
During instantiation, every cell (of 8 voxels) is checked to see whether this cell contains both a true and a false thresholded voxel.
v - Variable in class VolumeJ.VJBackprojection
 
v - Variable in class VolumeJ.VJUserInterface
 
v - Variable in class of3d.OF3DFlow
 
v - Variable in class of3d.OF3DDeformer
 
v - Variable in class volume.VolumeShort
 
v - Variable in class volume.VolumeInteger
 
v - Variable in class volume.VolumeFloat
 
v - Variable in class volume.Diffusion3D
 
v0i - Static variable in class FlowJ.FlowJSpotNoise
 
v0j - Static variable in class FlowJ.FlowJSpotNoise
 
v1i - Static variable in class FlowJ.FlowJSpotNoise
 
v1j - Static variable in class FlowJ.FlowJSpotNoise
 
valid(int, int) - Method in class FlowJ.FlowJFlow
 
valid(int, int) - Method in class volume.Volume
Check whether x,y are within the edges.
valid(int, int, int) - Method in class volume.Volume
Check whether x,y,z are within the edges.
valid(int, int, int, int) - Static method in class VolumeJ.VJTrilinear
Determine whether x,y are valid in an image width*height for bilinear interpolation.
valid(int, int, int, int) - Method in class volume.HyperVolume
 
valid(int, int, int, int, int) - Static method in class volume.Convolver
 
valid(int, int, int, int, int, int, int) - Static method in class volume.Convolver
 
validFileDescription(File) - Method in class io.OpenPreviewDialog
Return a descrpiptive String to display the file.
validFiles - Variable in class io.OpenPreviewDialog
 
value - Static variable in class FlowJ.FlowJSpotNoise
 
value - Variable in class of3d.OF3DSpot
 
VALUE - Static variable in class VolumeJ.VJClassifiers
 
value(byte[], int, int, int, float, float) - Static method in class VolumeJ.VJTrilinear
Bilinear interpolation at (ix+dx, iy+dy) of 2D image organised as byte[].
value(byte[], int, int, VJVoxelLoc) - Static method in class VolumeJ.VJTrilinear
Interpolate in a byte volume organized as a single array.
value(byte[], int, int, VJVoxelLoc) - Static method in class VolumeJ.VJNearestNeighbor
Interpolate in a byte volume organized as a single array.
value(float[][][][], int, VJVoxelLoc) - Static method in class VolumeJ.VJTrilinear
Interpolate in a float 4D hypervolume in a single dimension.
value(float[][][][], int, VJVoxelLoc) - Static method in class VolumeJ.VJNearestNeighbor
Interpolate in a float 4D hypervolume in a single dimension.
value(float[][][][], VJVoxelLoc, int) - Static method in class VolumeJ.VJNearestNeighbor
Interpolate an entry in a float vector volume.
value(float[][][][], VJVoxelLoc, int) - Static method in class of3d.FlowJTrilinearVector
Interpolate an entry in a float vector 4-D volume.
value(float[][][], VJVoxelLoc) - Static method in class VolumeJ.VJTrilinear
Interpolate in a float volume.
value(float[][][], VJVoxelLoc) - Static method in class VolumeJ.VJNearestNeighbor
Interpolate in a float volume.
value(float[], int, int, int, float, float) - Static method in class VolumeJ.VJTrilinear
Bilinear interpolation at (ix+dx, iy+dy) of 2D image organised as float[].
value(int[], int, int, int, float, float) - Static method in class VolumeJ.VJTrilinear
Bilinear interpolation of brightness at (ix+dx, iy+dy) of 2D image organised as int[].
value(OF3DFlow, VJVoxelLoc) - Method in class of3d.FlowJTrilinearVector
 
value(short[][][], VJVoxelLoc) - Static method in class VolumeJ.VJTrilinear
Interpolate in a short volume.
value(short[][][], VJVoxelLoc) - Static method in class VolumeJ.VJNearestNeighbor
Interpolate in a short volume.
value(short[], int, int, int, float, float) - Static method in class VolumeJ.VJTrilinear
Bilinear interpolation at (ix+dx, iy+dy) of 2D image organised as short[].
value(VJValue, Volume, VJVoxelLoc) - Method in class VolumeJ.VJInterpolator
Interpolate the value of v at location vl.
value(VJValue, Volume, VJVoxelLoc) - Method in class VolumeJ.VJTrilinear
Interpolate a volume.
value(VJValue, Volume, VJVoxelLoc) - Method in class VolumeJ.VJNearestNeighbor
Interpolate a volume.
valueHS(float[], Object[], int, VJVoxelLoc) - Static method in class VolumeJ.VJTrilinear
Interpolate hue and saturation in an RGB int volume organized as an array of slices.
valueHS(float[], Object[], int, VJVoxelLoc) - Static method in class VolumeJ.VJNearestNeighbor
Interpolate hue and saturation in an RGB int[][] volume organized as an array of slices.
valueHS(VJValueHSB, VolumeRGB, float, VJVoxelLoc) - Method in class VolumeJ.VJInterpolator
This method should not be here, but where: it is a special HSB vector interpolation for RGB volumes.
var(float[]) - Static method in class bijnum.BIJstats
Compute variance of all elements in vector v.
varianceSpectrum() - Method in class bijnum.BIJpca
Compute the accumulated variance spectrum.
vectorFromImageStack(ImagePlus, int) - Static method in class bijnum.BIJutil
Convert the data in the ImagePlus image stack into a float[] vector for further processing.
vectorFromImageStack(ImagePlus, int, float) - Static method in class bijnum.BIJutil
Convert the data in the ImageStack in imp into a float[][] matrix and scale by scaleFactor on the fly.
vectorFromImageStackRoi(ImagePlus) - Static method in class bijnum.BIJutil
Convert the data in the i'th ImagePlus image into a float[] vector for further processing.
vectorFromImageStackRoi(ImagePlus, int) - Static method in class bijnum.BIJutil
Convert the data in the i'th ImagePlus image into a float[] vector for further processing.
VERSION - Static variable in class VolumeJ.VJUserInterface
 
VERSION - Static variable in class VolumeJ.VJSurfaceJ
 
vertices(int, int, int) - Static method in class VolumeJ.VJCell
Compute the vertex coordinates of a cell at x, y, z.
viewspace - Variable in class VolumeJ.VJViewspaceRender
The viewspace buffer contains the x, y, z, and the interpolation coefficients steps for the next.
VIEWSPACE - Static variable in class VolumeJ.VJUserInterface
 
viewspacePixel - Variable in class VolumeJ.VJViewspaceRender
The viewspace pixel buffer contains the rgb composites and the alpha for all pixels.
visible() - Method in class VolumeJ.VJAlphaColor
 
visible(FlowJValue) - Method in class of3d.OFClassifierScintillansIx255
Tell calling program whether this voxel has an interesting index (worthy to do interpolation and gradient calcs on)
visible(FlowJValue) - Method in class of3d.OFClassifierScintillansNoFlow
Tell calling program whether this voxel has an interesting index (worthy to do interpolation and gradient calcs on)
visible(FlowJValue) - Method in class of3d.OFClassifierScintillansIxLT0
 
visible(VJValue) - Method in class VolumeJ.VJClassifier
Tell renderer whether this voxel will be visible.
visible(VJValue) - Method in class VolumeJ.VJClassifierIsosurface
 
visible(VJValue) - Method in class VolumeJ.VJClassifierLevoy
Tells renderer that all voxels are potentially visible.
visible(VJValue) - Method in class VolumeJ.VJClassifierLNotIndex0
Tell calling program whether this voxel has an interesting index (worthy to do interpolation and gradient calcs on) If the index == 0 (this classifier), the voxel will be skipped.
visible(VJValue) - Method in class of3d.OFClassifierScintillans
 
VJAlphaColor - class VolumeJ.VJAlphaColor.
This class is the abstract type for an alphacolor, i.e.
VJAlphaColor() - Constructor for class VolumeJ.VJAlphaColor
 
VJAlphaColor(float) - Constructor for class VolumeJ.VJAlphaColor
Use as a grayscale value container.
VJAlphaColor(float, float, float, float) - Constructor for class VolumeJ.VJAlphaColor
An alpha-grayscale value for float RGB values.
VJAlphaColor(float, int) - Constructor for class VolumeJ.VJAlphaColor
Use as an alpha-grayscale value container.
VJAlphaColor(float, int, int, int) - Constructor for class VolumeJ.VJAlphaColor
An alpha-grayscale value.
VJAlphaColor(int) - Constructor for class VolumeJ.VJAlphaColor
Use as a grayscale value container.
VJBackprojection - class VolumeJ.VJBackprojection.
VJBackprojection.
VJBackprojection() - Constructor for class VolumeJ.VJBackprojection
 
VJBinaryShell - class VolumeJ.VJBinaryShell.
VJBInaryShell.
VJBinaryShell() - Constructor for class VolumeJ.VJBinaryShell
 
VJBinaryShell(VJThresholdedVolume) - Constructor for class VolumeJ.VJBinaryShell
Create a binary shell out of a a thresholded volume
VJCell - class VolumeJ.VJCell.
VJCell.
VJCell(VJMatrix, VJMatrix) - Constructor for class VolumeJ.VJCell
A cell is the unit of a volume in isosurface rendering A cell consists of eight voxels, and has the same position as its lowerleftanterior voxel.
VJClassifier - class VolumeJ.VJClassifier.
This class is the superclass for all classifiers.
VJClassifier() - Constructor for class VolumeJ.VJClassifier
 
VJClassifierGradientCT - class VolumeJ.VJClassifierGradientCT.
This class implements the Gradient classification function with indexing for CT scans optimized.
VJClassifierGradientCT() - Constructor for class VolumeJ.VJClassifierGradientCT
 
VJClassifierInteger - class VolumeJ.VJClassifierInteger.
This class is the superclass for all VJ classifier that work on Integer voxel values.
VJClassifierInteger() - Constructor for class VolumeJ.VJClassifierInteger
 
VJClassifierIsosurface - class VolumeJ.VJClassifierIsosurface.
This class implements the classifier for colored isosurface rendering.
VJClassifierIsosurface() - Constructor for class VolumeJ.VJClassifierIsosurface
 
VJClassifierIsosurface(float) - Constructor for class VolumeJ.VJClassifierIsosurface
 
VJClassifierIsosurfaceGrayscale - class VolumeJ.VJClassifierIsosurfaceGrayscale.
This class implements the classifier for a grayscale isosurface renderer.
VJClassifierIsosurfaceGrayscale() - Constructor for class VolumeJ.VJClassifierIsosurfaceGrayscale
 
VJClassifierLevoy - class VolumeJ.VJClassifierLevoy.
This class implements the Levoy tent classification function with indexing.
VJClassifierLevoy() - Constructor for class VolumeJ.VJClassifierLevoy
Default instantiation.
VJClassifierLevoy(int, int, int) - Constructor for class VolumeJ.VJClassifierLevoy
Instantiation of new classifier.
VJClassifierLevoyCueing - class VolumeJ.VJClassifierLevoyCueing.
This class implements the Levoy tent classification function with depth cueing and indexing.
VJClassifierLevoyCueing() - Constructor for class VolumeJ.VJClassifierLevoyCueing
Default instantiation.
VJClassifierLinear - class VolumeJ.VJClassifierLinear.
This class implements a linear ramp classification function with indexing.
VJClassifierLinear() - Constructor for class VolumeJ.VJClassifierLinear
 
VJClassifierLNoIndex - class VolumeJ.VJClassifierLNoIndex.
This class implements the Levoy tent classification function without indexing.
VJClassifierLNoIndex() - Constructor for class VolumeJ.VJClassifierLNoIndex
 
VJClassifierLNotIndex0 - class VolumeJ.VJClassifierLNotIndex0.
This class implements the Levoy tent classification function with indexing.
VJClassifierLNotIndex0() - Constructor for class VolumeJ.VJClassifierLNotIndex0
 
VJClassifierRGB - class VolumeJ.VJClassifierRGB.
This class implements a classifier for RGB vector volumes.
VJClassifierRGB() - Constructor for class VolumeJ.VJClassifierRGB
 
VJClassifiers - class VolumeJ.VJClassifiers.
This class is a class whose only purpose is to contain all VJClassifier class definitions.
VJClassifiers() - Constructor for class VolumeJ.VJClassifiers
 
VJClassifierValue - class VolumeJ.VJClassifierValue.
This class implements a classification function on the voxel value only.
VJClassifierValue() - Constructor for class VolumeJ.VJClassifierValue
 
VJCutout - class VolumeJ.VJCutout.
VJCutout.
VJCutout(Volume, int, int, int, VJInterpolator, VJShader, VJClassifier) - Constructor for class VolumeJ.VJCutout
 
VJGradient - class VolumeJ.VJGradient.
This is a class that defines the gradient of a voxel.
VJGradient(double[]) - Constructor for class VolumeJ.VJGradient
 
VJGradient(double[][]) - Constructor for class VolumeJ.VJGradient
n-dimensional vector volume gradient.
VJGradient(double, double, double) - Constructor for class VolumeJ.VJGradient
Gradient of scalar volume.
VJGradient(float, float, float) - Constructor for class VolumeJ.VJGradient
Gradient of scalar volume.
VJInterpolator - class VolumeJ.VJInterpolator.
This class is the abstract class for all volume interpolators and defines the methods for each of these classes.
VJInterpolator() - Constructor for class VolumeJ.VJInterpolator
 
VJIsosurfaceRender - class VolumeJ.VJIsosurfaceRender.
VJIsosurfaceRender.
VJIsosurfaceRender(VJInterpolator, VJShader, VJClassifier) - Constructor for class VolumeJ.VJIsosurfaceRender
Create a new renderer with specified methods.
VJLight - class VolumeJ.VJLight.
This class implements a volume rendering light, and adds to methods to manipulate the light.
VJLight(float, float, float, float, float) - Constructor for class VolumeJ.VJLight
Create a new light.
VJMatrix - class VolumeJ.VJMatrix.
This class implements a transformation matrix and 3D transformation methods on it.
VJMatrix() - Constructor for class VolumeJ.VJMatrix
Create a new transformation matrix initialized to the unit matrix.
VJMatrix(float[][]) - Constructor for class VolumeJ.VJMatrix
Create a new transformation matrix from a float[][] matrix.
VJMatrix(VJMatrix) - Constructor for class VolumeJ.VJMatrix
Create a new transformation matrix initialized to another matrix.
VJNearestNeighbor - class VolumeJ.VJNearestNeighbor.
This class is the standard interpolator and implements nearest neighbor interpolation and interpolation of gradients.
VJNearestNeighbor() - Constructor for class VolumeJ.VJNearestNeighbor
 
VJOutlineShader - class VolumeJ.VJOutlineShader.
VJOutlineShader implements outline shading.
VJOutlineShader() - Constructor for class VolumeJ.VJOutlineShader
Create a new outline shader.
VJPhongShader - class VolumeJ.VJPhongShader.
VJShader implements shading in a Phong illumination model, for ambient and diffuse shading only.
VJPhongShader(float, VJLight, boolean) - Constructor for class VolumeJ.VJPhongShader
Create a new shader for ambient light and a VJLight light.
VJPlane - class VolumeJ.VJPlane.
VJPlane.
VJPlane(float[], float[], float[]) - Constructor for class VolumeJ.VJPlane
Create a new plane through 3 points p, q, r.
VJPlane(float[], float[], float[], VJMatrix) - Constructor for class VolumeJ.VJPlane
Create a new plane through 3 homogenuous coordinates p, q, r defined in a coordinate system, but define the plane in a transformation of that coordinate system defined by m.
VJPlane(VJPlane) - Constructor for class VolumeJ.VJPlane
Create a new plane from another plane.
VJPlane(VJPlane, float[]) - Constructor for class VolumeJ.VJPlane
Create a new plane parallel to a plane p through a point q.
VJProjection - class VolumeJ.VJProjection.
This class is a set of projections of an object.
VJProjection(double, Object[], int, int, int) - Constructor for class VolumeJ.VJProjection
Create a new projection.
VJReconstructor - class VolumeJ.VJReconstructor.
VJReconstructor reconstructs volumes in an ImageJ stack of any anisotropy along any axis.
VJReconstructor() - Constructor for class VolumeJ.VJReconstructor
 
VJRender - class VolumeJ.VJRender.
VJRender class.
VJRender(VJInterpolator, VJShader, VJClassifier) - Constructor for class VolumeJ.VJRender
Create a new classic renderer with specified methods.
VJRenderer - class VolumeJ.VJRenderer.
VJRenderer class implements the context and support methods for Volume Rendering.
VJRenderer(VJInterpolator, VJShader, VJClassifier) - Constructor for class VolumeJ.VJRenderer
Create a new default renderer with specified interpolator, shader and classifier.
VJRenderView - class VolumeJ.VJRenderView.
VJRenderView class implements a shell for rendering one or more views of a volume with a given renderer and volume.
VJRenderView(VJRenderer, double, double, double, double, String) - Constructor for class VolumeJ.VJRenderView
Instantiates a new rendering shell.
VJRenderView(VJRenderer, String) - Constructor for class VolumeJ.VJRenderView
Instantiates a new rendering shell.
VJRenderViewCine - class VolumeJ.VJRenderViewCine.
This subclass of VJRenderView implements cine mode rendering.
VJRenderViewCine(VJRenderer, float, float, float, float, String, int, boolean) - Constructor for class VolumeJ.VJRenderViewCine
Instantiates a new rendering shell: a wrapper for a VJRenderer to allow cine (multiple rotated views) renderings.
VJRenderViewInteractive - class VolumeJ.VJRenderViewInteractive.
VJRenderViewInteractive implements a shell for interactively modifying the view (by rotating etc).
VJRenderViewInteractive(ImagePlus, VJRenderer, double, String) - Constructor for class VolumeJ.VJRenderViewInteractive
Instantiates a new interactive render viewer.
VJRenderViewSingle - class VolumeJ.VJRenderViewSingle.
VJRenderView class implements a shell for viewing the one or more rendering of a volume with a given renderer.
VJRenderViewSingle(VJRenderer, double, double, double, double, String) - Constructor for class VolumeJ.VJRenderViewSingle
Instantiates a new rendering shell.
VJRenderViewStereo - class VolumeJ.VJRenderViewStereo.
VJRenderViewStereo is a subclass of VJRenderView that implements the shell for rendering two stereo views for viewing with a stereo viewer.
Copyright (c) 2001-2003, Michael Abramoff.
VJRenderViewStereo(VJRenderer, double, double, double, double, String) - Constructor for class VolumeJ.VJRenderViewStereo
 
VJrgbValue - class VolumeJ.VJrgbValue.
VJrgbValue.
VJrgbValue() - Constructor for class VolumeJ.VJrgbValue
 
VJrgbValue(int, int, int, int) - Constructor for class VolumeJ.VJrgbValue
Create a new VJrgbValue.
VJShade - class VolumeJ.VJShade.
VJShade.
VJShade(float) - Constructor for class VolumeJ.VJShade
 
VJShade(float, float, float) - Constructor for class VolumeJ.VJShade
 
VJShader - class VolumeJ.VJShader.
VJShader is the default null shader.
VJShader() - Constructor for class VolumeJ.VJShader
Create a new null shader.
VJShape - class VolumeJ.VJShape.
 
VJShape() - Constructor for class VolumeJ.VJShape
 
VJSplineInterpolator - class VolumeJ.VJSplineInterpolator.
This class implements cubic spline interpolation and interpolation of gradients.
VJSplineInterpolator() - Constructor for class VolumeJ.VJSplineInterpolator
 
VJSurfaceJ - class VolumeJ.VJSurfaceJ.
This class offers SurfaceJ, a surface plotting plugin based on VJ.
Copyright (c) 1999-2002, Michael Abramoff.
VJSurfaceJ() - Constructor for class VolumeJ.VJSurfaceJ
Open a new dialog.
VJSurfacePlotShell - class VolumeJ.VJSurfacePlotShell.
This class implements utility for surface plotting.
VJSurfacePlotShell(VJRenderer, float, float, float, float, Volume, float, float, float, float, String) - Constructor for class VolumeJ.VJSurfacePlotShell
Instantiates a new surface plotting rendering shell.
VJThresholdedVolume - class VolumeJ.VJThresholdedVolume.
This class creates thresholded (binary) volumes of any type of Volume.
VJThresholdedVolume() - Constructor for class VolumeJ.VJThresholdedVolume
creates the null volume.
VJThresholdedVolume(Volume, VJClassifier) - Constructor for class VolumeJ.VJThresholdedVolume
Create a new thresholded volume.
VJTrilinear - class VolumeJ.VJTrilinear.
This class implements trilinear voxel interpolation and voxel gradient interpolation.
VJTrilinear() - Constructor for class VolumeJ.VJTrilinear
 
VJUserInterface - class VolumeJ.VJUserInterface.
This class links the VJ classes to the ImageJ interface.
Copyright (c) 1999-2003, Michael Abramoff.
VJUserInterface() - Constructor for class VolumeJ.VJUserInterface
Open a new VJUserInterface.
VJValue - class VolumeJ.VJValue.
VJValue.
VJValue() - Constructor for class VolumeJ.VJValue
 
VJValue(float) - Constructor for class VolumeJ.VJValue
 
VJValue(VJValue) - Constructor for class VolumeJ.VJValue
 
VJValueHSB - class VolumeJ.VJValueHSB.
Contains an RGB volume voxel value in HSB format.
VJValueHSB() - Constructor for class VolumeJ.VJValueHSB
Create a new VJValueHSB.
VJValueHSB(float, float, float) - Constructor for class VolumeJ.VJValueHSB
Create a new VJValueHSB with hue, saturation and brightness set.
VJViewerCanvas - class VolumeJ.VJViewerCanvas.
This class is an interactive rendering viewer.
VJViewerCanvas(ImagePlus) - Constructor for class VolumeJ.VJViewerCanvas
Create a new VJViewerCanvas for imp.
VJViewspaceRender - class VolumeJ.VJViewspaceRender.
VJViewspaceRender class.
VJViewspaceRender(VJInterpolator, VJShader, VJClassifier) - Constructor for class VolumeJ.VJViewspaceRender
Create a new viewspace renderer with specified methods.
VJViewspaceUtil - class VolumeJ.VJViewspaceUtil.
VJViewspaceUtil implements viewspace utility methods, that can be used to relate a volume in a transformation matrix to the coordinates of that volume in viewspace.
VJViewspaceUtil() - Constructor for class VolumeJ.VJViewspaceUtil
 
VJVoxelLoc - class VolumeJ.VJVoxelLoc.
This class defines a voxel location for interpolation and rendering.
VJVoxelLoc() - Constructor for class VolumeJ.VJVoxelLoc
Empty VJVoxelLoc creator.
VJVoxelLoc(float[]) - Constructor for class VolumeJ.VJVoxelLoc
Create a new VJVoxelLoc from a vector.
VJVoxelLoc(float[], VJMatrix) - Constructor for class VolumeJ.VJVoxelLoc
Create a new VJVoxelLoc from a transformed vector location.
VJVoxelLoc(float, float, float) - Constructor for class VolumeJ.VJVoxelLoc
Create a new VJVoxelLoc for an objectspace location x,y,z.
VJVoxelLoc(float, float, float, VJMatrix) - Constructor for class VolumeJ.VJVoxelLoc
Create a new VJVoxelLoc from a transformed vector location.
VJZBuffer - class VolumeJ.VJZBuffer.
VJZBuffer.
VJZBuffer(int, int) - Constructor for class VolumeJ.VJZBuffer
Create a new VJZBuffer filled with 0.
VJZBuffer(int, int, double) - Constructor for class VolumeJ.VJZBuffer
Create a new VJZBuffer filled with 0.
volume - package volume
 
Volume - class volume.Volume.
This is an abstract super-class to implement volumes.
Volume() - Constructor for class volume.Volume
 
VolumeFloat - class volume.VolumeFloat.
This class implements float volumes and operations including convolutions on it.
VolumeFloat() - Constructor for class volume.VolumeFloat
creates the null volume.
VolumeFloat(float[][][]) - Constructor for class volume.VolumeFloat
Creates a float volume from a float vector with the same contents.
VolumeFloat(ImageProcessor) - Constructor for class volume.VolumeFloat
Creates a float volume 1 voxel deep from the contents of an ImageJ ImageProcessor.
VolumeFloat(ImageStack) - Constructor for class volume.VolumeFloat
Creates a float volume from an ImageJ ImageStack.
VolumeFloat(ImageStack, double, double, double) - Constructor for class volume.VolumeFloat
Creates a float volume from an ImageJ ImageStack.
VolumeFloat(ImageStack, int, int) - Constructor for class volume.VolumeFloat
Creates a float volume from an ImageJ ImageStack.
VolumeFloat(ImageStack, int, int, double, double, double) - Constructor for class volume.VolumeFloat
Creates a float volume from an ImageJ ImageStack.
VolumeFloat(int, int, int) - Constructor for class volume.VolumeFloat
Creates a float volume of defined size and default aspect ratios.
VolumeFloat(int, int, int, double, double, double) - Constructor for class volume.VolumeFloat
Creates a float volume of defined size and aspect ratio.
VolumeFloat(VolumeFloat) - Constructor for class volume.VolumeFloat
Creates a float volume which is an exact copy of vl.
VolumeInteger - class volume.VolumeInteger.
This class implements int volumes and operations including convolutions on it.
VolumeInteger() - Constructor for class volume.VolumeInteger
 
VolumeInteger(ImageProcessor) - Constructor for class volume.VolumeInteger
 
VolumeInteger(ImageStack) - Constructor for class volume.VolumeInteger
 
VolumeInteger(ImageStack, double, double, double) - Constructor for class volume.VolumeInteger
 
VolumeInteger(ImageStack, int, int) - Constructor for class volume.VolumeInteger
Creates a volume from an ImageStack, with depth slices from n * depth.
VolumeInteger(ImageStack, int, int, double, double, double) - Constructor for class volume.VolumeInteger
 
VolumeInteger(int, int, int) - Constructor for class volume.VolumeInteger
 
VolumeInteger(int, int, int, double, double, double) - Constructor for class volume.VolumeInteger
 
VolumeIO - class volume.VolumeIO.
This is a class that implements reading and writing on float volumes.
VolumeIO(int, int, int) - Constructor for class volume.VolumeIO
 
VolumeIO(String) - Constructor for class volume.VolumeIO
 
VolumeJ - package VolumeJ
 
VolumeRGB - class volume.VolumeRGB.
This class implements RGB vector volumes.
VolumeRGB(int, int, int, double, double, double) - Constructor for class volume.VolumeRGB
Creates an RGB volume of defined size and aspect ratio.
VolumeRGB(Object[], int, int, double, double, double) - Constructor for class volume.VolumeRGB
Creates an RGB volume of defined aspect ratio from an array of slices.
VolumeShort - class volume.VolumeShort.
This class implements short volumes and operations including convolutions on it.
VolumeShort() - Constructor for class volume.VolumeShort
creates the null volume.
VolumeShort(ImageStack) - Constructor for class volume.VolumeShort
Creates a short volume from an ImageJ ImageStack.
VolumeShort(ImageStack, double, double, double) - Constructor for class volume.VolumeShort
 
VolumeShort(ImageStack, int, int) - Constructor for class volume.VolumeShort
public VolumeShort(ImageProcessor ip) // Creates a volume with depth 1 from an ImageProcessor.
VolumeShort(ImageStack, int, int, double, double, double) - Constructor for class volume.VolumeShort
 
VolumeShort(int, int, int) - Constructor for class volume.VolumeShort
Creates a short volume of defined size and default aspect ratios.
VolumeShort(int, int, int, double, double, double) - Constructor for class volume.VolumeShort
Creates a short volume of defined size and aspect ratio.
VolumeShort(VolumeShort) - Constructor for class volume.VolumeShort
Creates a float volume which is an exact copy of vl.
vs - Variable in class of3d.OF3DFlow
 
vsv - Static variable in class VolumeJ.VJViewspaceRender
 
vsvstep - Static variable in class VolumeJ.VJViewspaceRender
 

W

w - Variable in class FlowJ.SSD
 
width - Variable in class FlowJ.FlowJSpotNoise
 
width - Variable in class VolumeJ.VJClassifierLevoy
 
width - Variable in class VolumeJ.VJReconstructor
 
width - Variable in class VolumeJ.VJRenderer
Boundaries of viewspace volume (the viewport) in k,j,i space.
width - Variable in class of3d.OF3DDeformer
 
width - Variable in class volume.Volume
Dimensions of the volume.
widthEllipse(float) - Method in class FlowJ.FlowJSpotNoise
 
widthField - Variable in class VolumeJ.VJUserInterface
 
windowActivated(WindowEvent) - Method in class io.OpenPreviewDialog
All events coming from Dialog window.
windowClosed(WindowEvent) - Method in class io.OpenPreviewDialog
 
windowClosing(WindowEvent) - Method in class VolumeJ.VJUserInterface
VJUserInterface has been closed.
windowClosing(WindowEvent) - Method in class io.OpenPreviewDialog
 
windowDeactivated(WindowEvent) - Method in class io.OpenPreviewDialog
 
windowDeiconified(WindowEvent) - Method in class io.OpenPreviewDialog
 
windowIconified(WindowEvent) - Method in class io.OpenPreviewDialog
 
windowOpened(WindowEvent) - Method in class io.OpenPreviewDialog
 
write(String) - Static method in class FlowJ.FlowJUserInterface
 
write(String) - Method in class FlowJ.FlowJFlow
Write the full flow field in Burkitt format into a file.
write(String) - Static method in class VolumeJ.VJUserInterface
Writes a string to an output channel.
write(String) - Method in class of3d.OF3DFlow
 
write(String) - Method in class volume.VolumeIO
 
write(StringBuffer) - Static method in class VolumeJ.VJUserInterface
Writes a string to an output channel.

X

x - Variable in class VolumeJ.VJVoxelLoc
 
xExpected(int, int) - Method in class FlowJ.FlowJError
 
xrot - Static variable in class VolumeJ.VJUserInterface
 

Y

y - Variable in class VolumeJ.VJVoxelLoc
 
yExpected(int, int) - Method in class FlowJ.FlowJError
 
yrot - Static variable in class VolumeJ.VJUserInterface
 

Z

z - Variable in class VolumeJ.VJVoxelLoc
 
zeroHistograms() - Method in class bijnum.BIJmi
 
zeromean(double[]) - Static method in class bijnum.BIJstats
Zero the mean of all elements of v.
zeromean(float[]) - Static method in class bijnum.BIJstats
Zero the mean of all elements of v.
zrot - Static variable in class VolumeJ.VJUserInterface
 

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
BIJ API

Submit a bug or feature

Copyright (c) 1997-2003 Michael Abramoff
Licensing available. All Rights Reserved.