< 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

<

() - Static method in class knn.ANN
Load the C++ ANN API library ann_java.dll, which should be in the mdasources ImageJ directory.

A

a - Variable in class bijfit.DesignMatrix
 
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.
a - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer
 
a - Static variable in class numericalMethods.geometry.latticeReduction.LLL
 
a - Variable in class registration.SearchMI
Two images.
A - Static variable in class net.sourceforge.jannealer.test.InverseObjectiveFunction
 
A - Static variable in class numericalMethods.geometry.latticeReduction.LLL
 
a2 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
a3 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
a4 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
a5 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
a6 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
abc - Static variable in class numericalMethods.calculus.minimizing.LineNDDBrent
 
abc - Static variable in class numericalMethods.calculus.minimizing.nmLineNDBrent
 
abs(float[]) - Static method in class bijnum.BIJmatrix
Return a vector with the absolutes of all elements in vector v.
absTol - Variable in class numericalMethods.calculus.integration.ExtrapIntegrator
 
AbstractValueCacher - class numericalMethods.function.util.AbstractValueCacher.
 
AbstractValueCacher.Key - class numericalMethods.function.util.AbstractValueCacher.Key.
 
AbstractValueCacher.Key(int) - Constructor for class numericalMethods.function.util.AbstractValueCacher.Key
 
AbstractValueCacher(int) - Constructor for class numericalMethods.function.util.AbstractValueCacher
 
ACC - Static variable in class numericalMethods.calculus.rootFinding.NewtonRaphson
Default accuracy: 1e-12.
accept(File) - Method in class io.DirFilter
 
accept(File) - Method in class retina.AcceptOID
 
accept(File, String) - Method in class retina.FilenameFilterAcceptOID
 
AcceptOID - class retina.AcceptOID.
Defines a FileFilter for KES OID files.
AcceptOID() - Constructor for class retina.AcceptOID
 
accuracy(float[]) - Static method in class bijnum.BIJstats
Compute accuracy or observed proportion of overall agreement of a test for which the result is in exp and the ground truth in truth accuracy = true pos + true neg / (true neg + false pos + true pos + false neg) accuracy = (a+d) / (a+b+c+d)
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.
accuracyMultipleClasses(int[][]) - Static method in class bijnum.BIJstats
Compute the accuracy of a test of which the confusion matrix is in tablenxn.
acqFinished() - Method in class va.VAInterface
 
acquirer - Variable in class va.VAInterface
 
acquiringFlag - Variable in class va.VAInterface
 
actionPerformed(ActionEvent) - Method in class FlowJ.FlowJUserInterface
 
actionPerformed(ActionEvent) - Method in class VolumeJ.VJUserInterface
React to action e.
actionPerformed(ActionEvent) - Method in class bd.BDUserInterface
 
actionPerformed(ActionEvent) - Method in class io.OpenPreviewDialog
 
actionPerformed(ActionEvent) - Method in class retina.PCAWindow
Act upon buttons pressed.
actionPerformed(ActionEvent) - Method in class retina.OIDReconstructor
 
actionPerformed(ActionEvent) - Method in class retina.OIDWindow
 
actionPerformed(ActionEvent) - Method in class va.VAInterface
 
activateButtons() - Method in class va.VAInterface
Activate the buttons, depending on the flags.
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(AbstractValueCacher.Key) - Method in class numericalMethods.function.util.AbstractValueCacher
 
add(double, double) - Method in class numericalMethods.function.util.DoubleValueCacher
 
add(double, double[], int) - Method in class numericalMethods.function.util.AbstractValueCacher
 
add(Feature) - Method in class knn.Features
Add the elements in newfeatures to features.
add(Feature[]) - Method in class knn.Features
Add the elements in newfeatures to features.
add(float[][], double) - Static method in class bijnum.BIJmatrix
Add a scalar to all entries in a matrix m in place.
add(float[][], float[]) - Method in class bijnum.BIJknn
Add extra data and classification to this knn.
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(Simplex) - Method in class net.sourceforge.jannealer.SimplexList
Add a Simplex object to the ArrayList
add(SSD, SSD) - Method in class FlowJ.SSD
 
add(Vector) - Method in class knn.Features
Deprecated.  
add(Vector, Feature) - Static method in class knn.Feature
Add the elements in newfeatures to features.
add(Vector, Feature[]) - Static method in class knn.Feature
Add the elements in newfeatures to features.
add(Vector, Vector) - Static method in class knn.Feature
Add the elements in newfeatures to features.
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
 
addFeature(Vector, String, double, int[][]) - Static method in class stereodisk.StereoDiskANNTester
 
addFeature(Vector, String, double, int[][]) - Static method in class stereodisk.StereoDiskROC
 
addOIDPanel() - Method in class retina.OIDWindow
 
addPanel() - Method in class retina.PCAWindow
Add the GUI items to this Window.
addPathTree(Vector, File) - Method in class io.OpenPreviewDialog
Add the whole path for File current to the end of v.
addPoint(double, double) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
addPoint(double, double, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
addPoint(double, double, int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
addPropertyChangeListener(PropertyChangeListener) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
addPropertyChangeListener(PropertyChangeListener) - Method in class numericalMethods.calculus.odeSolving.RungeKutta
 
addPropertyChangeListener(PropertyChangeListener) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
addPropertyChangeListener(PropertyChangeListener) - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
addPropertyChangeListener(PropertyChangeListener) - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
addToCharts(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
addToOldies(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
adjustmentValueChanged(AdjustmentEvent) - Method in class retina.PCAWindow
User has moved the slider on the StackWindow.
adjustmentValueChanged(AdjustmentEvent) - Method in class retina.OIDWindow
Inherited from StackWindow
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.
aggregate - Variable in class retina.OIDProcessor
The processed OID images.
aggregateCounter - Variable in class retina.ScriptProcessor
 
aggregateEpochs() - Method in class retina.OIDProcessor
Aggregate the frames in any number of epochs and return as a float[][].
aggregateFrames(float[][], float[][]) - Method in class retina.ScriptProcessor
Aggregate frames (add in the correct order) in experiment into the existing image array a.
aggregateFrames(ImagePlus, float[][]) - Method in class retina.ScriptProcessor
Aggregate frames (add in the correct order) in imp into the existing image array a.
aggregateRegistration - Variable in class retina.OIDProcessor
Registration parameters for aggregate, null if no registration was performed.
AGGREGATESAVE - Static variable in class retina.ScriptProcessor
 
aggregating - Variable in class retina.OIDProcessor
 
alf - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer
 
algorithmChoice - Variable in class bd.BDUserInterface
 
alignmentTimecourseAnalysis(float[][], int, int) - Static method in class retina.OIDAnalysis
Do timecourse analysis of all alignment (motion) parameters of each frame.
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.
amebsa(double, double, long) - Method in class net.sourceforge.jannealer.Schedule
Multi-dimensional minimization algorithm.
amotsa(int, int, double, double, long, double) - Method in class net.sourceforge.jannealer.Schedule
Extrapolation through the face of the Simplex
an - Variable in class bijnum.BIJpca
 
analysisTime - Variable in class retina.OIDamplitudeAnalyzer
Moment after start of stimulus when you want to examine amplitude of signal.
ANALYZE - Static variable in class retina.ScriptProcessor
 
ANALYZE_AMPLITUDE - Static variable in class retina.ScriptProcessor
 
ANALYZE_AUTOSCALING - Static variable in class retina.ScriptProcessor
 
ANALYZE_BAG - Static variable in class retina.ScriptProcessor
 
ANALYZE_CONDS - Static variable in class retina.ScriptProcessor
 
ANALYZE_FIRSTFRAME - Static variable in class retina.ScriptProcessor
 
ANALYZE_FOVEAX - Static variable in class retina.ScriptProcessor
 
ANALYZE_FOVEAY - Static variable in class retina.ScriptProcessor
 
ANALYZE_MASKFILE - Static variable in class retina.ScriptProcessor
 
ANALYZE_PCA - Static variable in class retina.ScriptProcessor
 
ANALYZE_REGISTER - Static variable in class retina.ScriptProcessor
 
ANALYZE_REGISTER_ROISIZE - Static variable in class retina.ScriptProcessor
 
ANALYZE_REGISTER_ROIX - Static variable in class retina.ScriptProcessor
 
ANALYZE_REGISTER_ROIY - Static variable in class retina.ScriptProcessor
 
ANALYZE_ROI - Static variable in class retina.ScriptProcessor
 
ANALYZE_ROITC - Static variable in class retina.ScriptProcessor
 
ANALYZE_START - Static variable in class retina.ScriptProcessor
 
ANALYZE_TIMECOURSE - Static variable in class retina.ScriptProcessor
 
ANALYZE_USECOND - Static variable in class retina.ScriptProcessor
 
analyze(BIJpca, int, String, String) - Static method in class retina.OIDtc
Analyze a series of OID frames a.
analyze(float[][], float[][], int, String, String) - Method in class retina.OIDAnalyzer
Analyze a series of OID frames a.
analyze(float[][], float[][], int, String, String) - Method in class retina.OIDTimecourseAnalyzer
 
analyze(float[][], float[][], int, String, String) - Method in class retina.OIDTimecourseStimulatedAnalyzer
Analyze a series of OID frames a and show timecourse of stimulated area reflectanc relative to non stimulated area for all frames.
analyze(float[][], float[][], int, String, String) - Method in class retina.OIDMapsFitter
Basically do nothing except create the fitted maps.
analyze(float[][], float[][], int, String, String) - Method in class retina.OIDroiAnalyzer
Analyze a series of OID frames a.
analyze(float[][], float[][], int, String, String) - Method in class retina.OIDPCAAnalyzer
Analyze a series of OID frames a.
analyze(float[][], float[][], int, String, String) - Method in class retina.OIDROItimecourseAnalyzer
Analyze a series of OID frames a.
analyze(float[][], float[][], int, String, String) - Method in interface retina.OIDBaseAnalyzer
 
analyze(float[][], float[][], int, String, String) - Method in class retina.OIDffAllAnalyzer
Analyze a series of OID frames a.
analyze(float[][], int, String, String) - Method in class retina.OIDroiTCAnalyzer
Analyze a series of OID frames a.
analyze(float[][], int, String, String) - Method in class retina.OIDbaselineAnalyzer
Analyze a series of OID frames a.
analyze(float[][], int, String, String) - Method in class retina.OIDamplitudeAnalyzer
Analyze series of OID frames a.
analyze(float[][], int, String, String) - Method in class retina.OIDAverageAnalyzer
Analyze a series of OID frames a.
analyzeBags(float[], float[], int) - Static method in class retina.OIDAnalysis
Analyze two arrays of pixel values by calculating their ratio and the standard error of the ratio.
analyzeProbabilities(float[][], float[][], int, Vector) - Static method in class stereodisk.StereoDiskAnalyzer
Determine the probabilities that a pixelfeature can differentiate between two classes for all classes and all features.
analyzer - Variable in class retina.ScriptProcessor
 
analyzeTimecourse(float[], String) - Method in class retina.PCAWindow
Analyze the coordinates of the PCA basis (the time courses of the components), with a timecourse vector t.
AngiographAnalyzer - class retina.AngiographAnalyzer.
Angiograph analyzer.
AngiographAnalyzer() - Constructor for class retina.AngiographAnalyzer
 
angle - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel
 
AngleOptimization2D - class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D.
 
AngleOptimization2D(int[], boolean[]) - Constructor for class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
AngleOptimization2D(int[], int[], int) - Constructor for class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
angleS - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel
 
angleT - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel
 
ANN - class knn.ANN.
API for interface to ANN (Approximate Nearest Neighbor) classification.
ANN() - Constructor for class knn.ANN
 
anneal() - Method in class net.sourceforge.jannealer.AnnealingScheme
runs an annealing, call getOffset() to get result
AnnealingScheme - class net.sourceforge.jannealer.AnnealingScheme.
Implements downhill simplex simulated annealing algorithm
AnnealingScheme() - Constructor for class net.sourceforge.jannealer.AnnealingScheme
 
annkEstimates(float[], float[][], int, int, double, float[]) - Static method in class knn.ANN
 
annkPriSearch(float[], int, int[], float[], double) - Static method in class knn.ANN
 
applyTo(int[], int) - Static method in class numericalMethods.algebra.group.Permutation
Returns j such that s[j]==i.
applyToFun(int[], int) - Static method in class numericalMethods.algebra.group.Permutation
Returns s[i].
area - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel
 
areaS - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel
 
areaT - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel
 
arrayLeftDivide(Matrix) - Method in class Jama.Matrix
Element-by-element left division, C = A.\B
arrayLeftDivideEquals(Matrix) - Method in class Jama.Matrix
Element-by-element left division in place, A = A.\B
arrayRightDivide(Matrix) - Method in class Jama.Matrix
Element-by-element right division, C = A./B
arrayRightDivideEquals(Matrix) - Method in class Jama.Matrix
Element-by-element right division in place, A = A./B
Arrays - class numericalMethods.util.Arrays.
This class provides utilities for arrays as static methods.
arrayTimes(Matrix) - Method in class Jama.Matrix
Element-by-element multiplication, C = A.*B
arrayTimesEquals(Matrix) - Method in class Jama.Matrix
Element-by-element multiplication in place, A = A.*B
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.
assign(double[][], double) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns all entries of matrix A with value.
assign(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assign matrix B to matrix A.
assign(double[], double) - Static method in class numericalMethods.algebra.linear.VectorOperations
Assign vector a to scalar v.
assign(double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Assign vector a to scalar b.
assign(int[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assign matrix B to matrix A.
assign(int[][], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns all entries of matrix A with value.
assign(int[][], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assign matrix B to matrix A.
assign(int[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Assign vector b to vector a.
assign(int[], int) - Static method in class numericalMethods.algebra.linear.VectorOperations
Assign vector a to scalar v.
assign(int[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Assign vector b to vector a.
assignCol(double[][], double[], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the column of matrix A with vector v.
assignCol(double[][], int[], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the column of matrix A with vector v.
assignCol(int[][], int[], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the column of matrix A with vector v.
assignDiagonal(double[][], double) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the diagonal of matrix A with v.
assignDiagonal(double[][], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the diagonal of matrix A with v.
assignDiagonal(double[][], int[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the diagonal of matrix A with v.
assignDiagonal(int[][], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the diagonal of matrix A with v.
assignDiagonal(int[][], int[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the diagonal of matrix A with v.
assignId(double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Makes matrix A to id.
assignId(int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Makes matrix A to id.
assignRow(double[][], double[], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the row of matrix A with vector v.
assignRow(double[][], int[], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the row of matrix A with vector v.
assignRow(int[][], int[], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the row of matrix A with vector v.
assignZero(double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Assign vector a to zero.
assignZero(double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns all entries of matrix A with zero.
assignZero(int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Assign vector a to zero.
assignZero(int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns all entries of matrix A with zero.
at(int, int, int) - Method in class VolumeJ.VJShape
 
attenuate(VJShade) - Method in class VolumeJ.VJAlphaColor
 
aTuple - Static variable in class numericalMethods.calculus.minimizing.LineNDDBrent
 
aTuple - Static variable in class numericalMethods.calculus.minimizing.nmLineNDBrent
 
autocorr(double[], int) - Static method in class bijnum.BIJstats
Computes autocorrelation up to maxk for the time series data.
autocov(double[], int) - Static method in class bijnum.BIJstats
Computes autocovariance up to maxk for the time series data.
average(double[]) - Static method in class numericalMethods.calculus.integration.NewtonCotes
 
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.
averageCalculate(float[][], int, int, int, int, int, float[]) - Static method in class retina.OIDAnalysis
Calculate the average frame for a number of frames based on a mask for all repeats.
averageMagnitude() - Method in class FlowJ.FlowJFlow
Return the length of the previously computed average flow.
averageOverVelocity() - Method in class FlowJ.FlowJError
 
avg(double[]) - Static method in class bijnum.BIJstats
Compute average of all values in vector v.
avg(float[]) - Static method in class bijnum.BIJstats
Compute average of all values in vector v.
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
 
avgDur - Variable in class retina.OIDWindow
 
avgNoExtremes(float[], float) - Static method in class bijnum.BIJstats
 
avgPre - Variable in class retina.OIDWindow
 
AXB - class numericalMethods.algebra.linear.solve.AXB.
Computes for a system of equations A·X=B with given matrices A and B the solving or minimizing matrix X.
AXB() - Constructor for class numericalMethods.algebra.linear.solve.AXB
 
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 registration.SearchMI
 
b - Variable in class volume.VolumeRGB
The brightness of each voxel as a byte (0-225).
B - Static variable in class net.sourceforge.jannealer.test.InverseObjectiveFunction
 
b21 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b31 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b32 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b41 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b42 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b43 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b51 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b52 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b53 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b54 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b61 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b62 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b63 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b64 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
b65 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
backCheckbox - Variable in class VolumeJ.VJUserInterface
 
backproject(Volume) - Method in class VolumeJ.VJProjection
Backprojection around a single axis y.
bad(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
bag - Static variable in class retina.OIDAnalyzer
 
bag - Static variable in class retina.OIDTimecourseAnalyzer
 
bag - Static variable in class retina.OIDROItimecourseAnalyzer
 
bagAlignment - Static variable in class retina.OIDTimecourseAnalyzer
 
bagPixels(float[][], int, int, int, float[], int, int, float[], float[]) - Static method in class retina.OIDAnalysis
Collect all pixels in into arrays aggrPixelsStim respectively aggrPixelsNonStim using a mask, where pixels with mask = 1 go into aggrPixelsStim and pixels with mask = -1 go into aggrPixelsNonStim, pixels with mask = 0 are ignored.
bagPixels(float[][], int, int, int, int, int, float[]) - Static method in class retina.OIDAnalysis
Collect all pixels into an array aggrPixels Only pixels in the frames belonging to unique condition j are collected.
balanced - Static variable in class stereodisk.StereoDiskANNTester
 
balanced - Static variable in class stereodisk.StereoDiskROC
 
baselineAnalysis(float[][], int, int, int, int, int) - Static method in class retina.OIDAnalysis
Do baseline frame analysis on each frame in a separately.
bcomposite - Static variable in class FlowJ.FlowJSpotNoise
 
bd - package bd
 
BDColorSeparator - class bd.BDColorSeparator.
 
BDColorSeparator(ColorProcessor, int, int, BDSeparatorLattice) - Constructor for class bd.BDColorSeparator
 
BDRedWhiteLattice - class bd.BDRedWhiteLattice.
 
BDRedWhiteLattice() - Constructor for class bd.BDRedWhiteLattice
 
BDSeparatorLattice - class bd.BDSeparatorLattice.
 
BDSeparatorLattice() - Constructor for class bd.BDSeparatorLattice
 
bdtree(float[][], int) - Static method in class knn.ANN
Train a ANN classifier (bd_tree).
BDUserInterface - class bd.BDUserInterface.
This class links the BD classes.
BDUserInterface() - Constructor for class bd.BDUserInterface
 
BDVarDetector - class bd.BDVarDetector.
 
BDVarDetector(ImageProcessor, int, int) - Constructor for class bd.BDVarDetector
 
BDYellowLattice - class bd.BDYellowLattice.
 
BDYellowLattice() - Constructor for class bd.BDYellowLattice
 
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
 
BIJfft - class bijnum.BIJfft.
This class implements a one-dimensional real->complex fast fourier transform Copyright (c) 1999-2004, Michael Abramoff.
BIJfft(double[]) - Constructor for class bijnum.BIJfft
Set up a BIJfft a matrix x of length power of 2.
BIJfft(float[]) - Constructor for class bijnum.BIJfft
Set up a BIJfft a matrix x of length power of 2.
BIJfht - class bijnum.BIJfht.
This class implements the fast Hartley transform on matrices and vectors (real float matrices).
BIJfht(int) - Constructor for class bijnum.BIJfht
Set up a BIJfht for matrices of size length = maxNxmaxN
bijfit - package bijfit
 
BIJfit - class bijnum.BIJfit.
This class implements useful linear and polynomial regression from Press, Flannery, Teukolsky, Vetterling, Numerical Recipes in C 2nd ed, Cambridge University Press, 1986 Copyright implementation (c) 1999-2004, Michael Abramoff.
BIJfit() - Constructor for class bijnum.BIJfit
 
BIJfunctions - class bijnum.BIJfunctions.
This class implements useful numerical functions from Press, Flannery, Teukolsky, Vetterling, Numerical Recipes in C 2nd ed, Cambridge University Press, 1986 Copyright implementation (c) 1999-2004, Michael Abramoff.
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
 
BIJknn(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 .
bin(double[], int) - Static method in class bijnum.BIJutil
Bin a vector x.
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
 
binTranspose(float[][], int, int) - Static method in class retina.AngiographAnalyzer
Bin each column of matrix a for bin size n and transpose the resulting matrix.
BirkhoffFactorization - class numericalMethods.algebra.loopGroup.BirkhoffFactorization.
Computes the Birkhoff factorization of a GL_n(C)-valued loop X = X1 X2.
BirkhoffFactorization() - Constructor for class numericalMethods.algebra.loopGroup.BirkhoffFactorization
 
bitrev - Variable in class bijnum.BIJfht
 
bitrev(int) - Method in class bijnum.BIJfft
 
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
 
BLINKDEV - Static variable in class retina.OIDProcessor
Number of standarddeviations from average eye-motion to qualify as abnormal or blink.
BlobDetector - class bd.BlobDetector.
 
BlobDetector(ImageProcessor, int, int) - Constructor for class bd.BlobDetector
 
BLOCK - Static variable in class retina.OIDProcessor
 
BLOCK - Static variable in class retina.OIDAnalysis
 
blockAnalysis(float[][][], int, String, String, String[], int, int) - Static method in class retina.OIDAnalysis
Analyze r blockwise.
BoundingBox - class numericalMethods.geometry.bounding.BoundingBox.
Provides static method for computing bounding box for point clouds.
BoundingBox() - Constructor for class numericalMethods.geometry.bounding.BoundingBox
Protect constructor since it is static only class.
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.
buildString(String[]) - Static method in class stereodisk.StereoDiskAnalyzer
 
BulirschStoer - class numericalMethods.calculus.odeSolving.BulirschStoer.
 
BulirschStoer.TempDataContainer - class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer.
 
BulirschStoer.TempDataContainer(double) - Constructor for class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer
 
BulirschStoer() - Constructor for class numericalMethods.calculus.odeSolving.BulirschStoer
 
BulirschStoer(int) - Constructor for class numericalMethods.calculus.odeSolving.BulirschStoer
 
BulirschStoerIntegrator - class numericalMethods.calculus.integration.BulirschStoerIntegrator.
 
BulirschStoerIntegrator() - Constructor for class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
BulirschStoerIntegrator(DoubleParametrized, DoubleArrayValued) - Constructor for class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
BulirschStoerIntegrator(DoubleParametrized, DoubleArrayValued, boolean) - Constructor for class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
BulirschStoerIntegrator(int) - Constructor for class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
BulirschStoerIntegrator(int, boolean) - Constructor for class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
buttonAcq - Variable in class va.VAInterface
 
buttonClose - Variable in class va.VAInterface
 
buttonCopy - Variable in class retina.PCAWindow
 
buttonMapAll - Variable in class retina.PCAWindow
 
buttonMapCleaned - Variable in class retina.PCAWindow
 
buttonMapCoordinates - Variable in class retina.PCAWindow
 
buttonMapIndicatorFunction - Variable in class retina.PCAWindow
 
buttonMapTruncDif - Variable in class retina.PCAWindow
 
buttonProjectImage - Variable in class retina.PCAWindow
 
buttonProjectTimecourse - Variable in class retina.PCAWindow
 
buttonRingAcq - Variable in class va.VAInterface
 
buttonSave - Variable in class retina.OIDWindow
 
buttonSort - Variable in class retina.OIDReconstructor
 
buttonSortNonStimulus - Variable in class retina.OIDReconstructor
 
buttonSpectrum - Variable in class retina.PCAWindow
 
buttonStart - Variable in class va.VAInterface
 
buttonStop - Variable in class va.VAInterface
 
buttonSubtractAll - Variable in class retina.OIDWindow
 
buttonTimecourse - Variable in class retina.OIDWindow
Number of standarddeviations from average eye-motion to qualify as abnormal or blink.
buttonTimeCourses - Variable in class retina.PCAWindow
 
byteHeader - Variable in class retina.OIDHeader
 

C

C - Variable in class bijnum.BIJfht
Static variables used in BIJfht algorithms.
C - Variable in class bijnum.BIJfft
 
C - Static variable in class numericalMethods.calculus.minimizing.Golden
 
c1 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
c3 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
c4 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
c6 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
cacher - Variable in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
cachValues - Variable in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
calcDeg(double[], double[], int) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
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
 
cashKarpErrorExtimate(DoubleArrayParametrized, DoubleArrayValued, double[], double[], double, double[], double[], double[][]) - Static method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
CATALAN - Static variable in class numericalMethods.calculus.specialFunctions.TestClausen
 
CATALAN - Static variable in class numericalMethods.calculus.specialFunctions.Clausen
Catalan's constant G.
center(float[], int, float[], int, float) - Static method in class bijnum.BIJutil
Center a scaled image1 into the center of a larger image0.
center(float[], int, float[], int, float, int, int) - Static method in class bijnum.BIJutil
Center a scaled image1 into the center of a larger image0 with offset offset_x and offset_y.
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
 
CGOLD - Static variable in class numericalMethods.calculus.minimizing.nmBrent
 
CGOLD - Static variable in class numericalMethods.calculus.minimizing.DBrent
 
CGOLD - Static variable in class numericalMethods.calculus.minimizing.ConjugateGradient
 
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
 
charts - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
ChebyshevApproximation - class numericalMethods.calculus.functionApproximation.ChebyshevApproximation.
A class that provides static methods related to the approximation of functions with Chebyshev polynomials.
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
 
checkAvg - Variable in class retina.OIDReconstructor
 
checkFaceArray() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
checkFaceArray() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
checkForCharts() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
checkForCharts(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
checkForNewEdges(double, double, double, double, double, double, int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
checkinverse(double[][], double[][]) - Static method in class bijnum.BIJmatrix
Check whether JI is really the inverse of J.
checkLast2 - Variable in class retina.OIDReconstructor
 
checkLinearCorrect - Variable in class retina.OIDReconstructor
 
checkPointArray() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
checkReg - Variable in class retina.OIDReconstructor
 
checkResultsDirectory(String) - Static method in class retina.ScriptProcessor
Check whether directoryResults exists.
checkSegment(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
checkSegments() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
checkSegments(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
checkShape(double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Throw IllegalArgumentException if v' length does not equal w' length.
checkShape(double[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Throw IllegalArgumentException if v' length does not equal w' length.
checkShape(int[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Throw IllegalArgumentException if v' length does not equal w' length.
checkShape(int[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Throw IllegalArgumentException if v' length does not equal w' length.
checkSubOpp - Variable in class retina.OIDReconstructor
 
checkTriangle(int, double, double) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
choiceDir - Variable in class io.OpenPreviewDialog
 
chol() - Method in class Jama.Matrix
Cholesky Decomposition
Cholesky - class numericalMethods.algebra.linear.decompose.Cholesky.
Computes the cholesky decomposition of a symmetric positive-definite Matrix and can therefore test whether a symmetric matrix is positive-definite.
CholeskyDecomposition - class Jama.CholeskyDecomposition.
Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class Jama.CholeskyDecomposition
Cholesky algorithm for symmetric and positive definite matrix.
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
 
circleR - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
circleTransform(float[], int, double) - Method in class registration.HoughTransform
Hough transform the image for a circle with radius.
circleX - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
circleY - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
cl - Static variable in class numericalMethods.calculus.specialFunctions.TestClausen
 
cl2(double) - Static method in class numericalMethods.calculus.specialFunctions.Clausen
Clausens integral Cl2.
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
 
classifiers - Variable in class bd.BDUserInterface
 
classifierTextArea - Variable in class VolumeJ.VJUserInterface
 
classify(float[][], int) - Method in class bijnum.BIJknn
Find the classification of M (N dimensional) vectors unknown in the dataset.
classset - Variable in class bijnum.BIJknn
The corresponding classification for each vector in the dataset, a 1xM vector.
Clausen - class numericalMethods.calculus.specialFunctions.Clausen.
A class providing Clausen's integral and Catalans constant.
clean(double) - Static method in class bijnum.BIJtransform
 
clear() - Method in class numericalMethods.function.util.AbstractValueCacher
 
clickTime - Variable in class VolumeJ.VJViewerCanvas
Some practical variables
clipboard(PrintWriter) - Method in class FlowJ.FlowJError
 
clone() - Method in class Jama.Matrix
Clone the Matrix object.
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
 
ComplexLaurentPolynomial - class numericalMethods.algebra.polynomial.ComplexLaurentPolynomial.
This is provides routines for complex laurent polynomials.
ComplexLaurentPolynomial() - Constructor for class numericalMethods.algebra.polynomial.ComplexLaurentPolynomial
 
ComplexPolynomial - class numericalMethods.algebra.polynomial.ComplexPolynomial.
This is provides routines for complex polynomials.
ComplexPolynomial() - Constructor for class numericalMethods.algebra.polynomial.ComplexPolynomial
 
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.
compressed - Variable in class va.ThreadCompression
 
compressZIP(short[]) - Method in class va.VideoAcq
Compress the image using ZIP compression.
compute() - Method in class bd.BlobDetector
 
compute() - Method in class bd.BDColorSeparator
 
compute() - Method in class bd.BDVarDetector
 
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(double[][]) - Static method in class numericalMethods.algebra.linear.Determinant
Computes the determinant of a real valued square matrix.
compute(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.Determinant
Computes the determinant of a complex valued square matrix.
compute(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.Inversion
Inverts a real valued square matrix.
compute(double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.Inversion
Inverts a complex valued square matrix.
compute(double[][], double[][], double[][], double[][], double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.Inversion
Inverts a complex valued square matrix.
compute(double[][], double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.Inversion
Inverts a real valued square matrix.
compute(double[][], double[][], int[]) - Static method in class numericalMethods.algebra.linear.Determinant
Computes the determinant of a complex valued square matrix.
compute(double[][], int[]) - Static method in class numericalMethods.algebra.linear.Determinant
Computes the determinant of a real valued square matrix.
compute(double[], int, double[][], double[], double[]) - Static method in class numericalMethods.geometry.bounding.BoundingBox
Computes bounding box for point cloud in arbitrary dimension.
compute(float) - Method in class VolumeJ.VJShade
Compute the value of contribution after shading with this shade.
compute(float[]) - Method in class bijnum.BIJfft
Compute the 1-D Fast fourier transform for x.
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.
compute(int[][], float[], int) - Method in class registration.HoughTransform
Use the accumulator a (0-amax) to count the number of occurences, and return in the values array.
compute(int, ColorProcessor, ColorProcessor, float[]) - Static method in class knn.FeatureComputer
Compute a feature.
compute1(FlowJFlow, float) - Method in class FlowJ.FlowJSingh
 
compute2(float[]) - Method in class bijnum.BIJfft
 
compute2(FlowJFlow, float) - Method in class FlowJ.FlowJSingh
 
compute3D() - Method in class volume.Diffusion3D
 
compute4D() - Method in class volume.Diffusion3D
 
computeAngleAndArea() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
computeAngleAndArea(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
computeCircumCircle(double, double, double, double, double, double) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
computeCircumCircle(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
computeConditionDeltas(BIJpca, int, int, float[]) - Static method in class retina.OIDAnalysis
Compute deltas, the difference of the means of the time-coordinates an's over the conditions stimulus = ON and stimulus = OFF.
computed - Variable in class of3d.OF3DFlow
 
computeDeltas(float[]) - Method in class retina.PCAWindow
Compute deltas, the difference of the means of the time-coordinates an's over the conditions s = -1 and s = +1.
computeEigenimages() - Method in class bijnum.BIJpca
Compute the spatial eigenimages, i.e.
computeFramesSummation(float[][], int, int, int, int, int, int) - Static method in class retina.OIDAnalysis
 
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
 
computeInteriorPoint(double[]) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
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.
computeMean(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
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.
computeTruncationContributions(BIJpca, float[], int, int, int, int, int, int, int, double) - Static method in class retina.OIDAnalysis
Compute the truncation factors for pca and the confidenceLimit for a single condition.
computeVarDeriv() - Method in class bd.BDVarDetector
 
concat(double[], double[], double[]) - Static method in class numericalMethods.util.Arrays
Retuns an array containing the contents of con and cat.
concat(float[], float[]) - Static method in class bijnum.BIJmatrix
Concatenate a vector to another vector in the same order.
concat(float[], float[], float[]) - Static method in class numericalMethods.util.Arrays
Retuns an array containing the contents of con and cat.
concat(int[], int[], int[]) - Static method in class numericalMethods.util.Arrays
Retuns an array containing the contents of con and cat.
concatFileName - Static variable in class retina.EpochSorter
 
cond() - Method in class Jama.SingularValueDecomposition
Two norm condition number
cond() - Method in class Jama.Matrix
Matrix condition (2 norm)
conditionAnalysis(float[][][], float[][], int) - Static method in class retina.OIDAnalysis
Condition analysis of timecourse data.
condStrings - Variable in class retina.ScriptProcessor
Contains the condition names.
confidence - Variable in class registration.LocatedCircle
 
CONFIDENCELIMIT - Static variable in class retina.ScriptProcessor
 
ConfigureAnnealing - class net.sourceforge.jannealer.test.ConfigureAnnealing.
Use simulated annealing to find the best configuration of simulated annealing.
ConfigureAnnealing() - Constructor for class net.sourceforge.jannealer.test.ConfigureAnnealing
 
confMax - Variable in class retina.PCAWindow
 
confs - Variable in class retina.PCAWindow
 
ConjugateGradient - class numericalMethods.calculus.minimizing.ConjugateGradient.
 
ConjugateGradient() - Constructor for class numericalMethods.calculus.minimizing.ConjugateGradient
 
constructWithCopy(double[][]) - Static method in class Jama.Matrix
Construct a matrix from a copy of a 2-D array.
containsNaN(float[]) - Static method in class bijnum.BIJmatrix
 
containsNaN(float[][]) - Static method in class bijnum.BIJmatrix
 
contract(int, int) - Method in class net.sourceforge.jannealer.Schedule
Contraction utility
CONTRAST - Static variable in class retina.OIDProcessor
 
CONTRAST - Static variable in class retina.OIDAnalysis
 
controlMasks - Static variable in class retina.OIDroiAnalyzer
 
convertImageToResult(ColorProcessor) - Static method in class stereodisk.StereoDiskConventions
Convert a colorprocessor with an image containing different colors for different classes into an array with 0...number of classes for each pixel.
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
 
coolingRate - Variable in class net.sourceforge.jannealer.AnnealingScheme
 
copy - Variable in class retina.OIDWindow
 
copy() - Method in class Jama.Matrix
Make a deep copy of a matrix
copy(double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Returns a clone of vector a.
copy(double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Returns a copy of matrix A.
copy(float[]) - Static method in class bijnum.BIJmatrix
Copy a vector.
copy(float[][]) - Static method in class bijnum.BIJmatrix
Copy a matrix.
copy(int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Returns a copy of vector a.
copy(int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Returns a copy of matrix A.
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.
Correlator - class registration.Correlator.
This class implements static methods for cross-correlating images.
Correlator() - Constructor for class registration.Correlator
 
Cos - class numericalMethods.calculus.minimizing.Cos.
 
Cos() - Constructor for class numericalMethods.calculus.minimizing.Cos
 
cosAngle - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
cosAngle - Variable in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
cosAngle(int, int) - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
cosLeastAngle - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
cosLeastAngle() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
cosMinAngle - Variable in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
count - Variable in class bd.BDUserInterface
 
count - Variable in class net.sourceforge.jannealer.test.InverseObjectiveFunction
 
count() - Method in class bd.BlobDetector
 
covariance(float[][], boolean) - Static method in class bijnum.BIJstats
Compute the covariance matrix for a matrix of size NxM.
createBalancedSampleBlock(float[], int) - Static method in class stereodisk.StereoDiskAnalyzer
Kreeer een block van n x,y coordinaten waarmee de kans zo hoog mogelijk is om 1:1:1 van de 3 classificaties te vangen.
createBalancedSampleBlocks(float[][], int) - Static method in class stereodisk.StereoDiskAnalyzer
Create as many blocks of balanced pixel indices as there are images in images.
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.
CreateChoice(Panel, String, String[], int) - Method in class bd.BDUserInterface
 
createPixelSet(float[][], int[][], String) - Static method in class stereodisk.StereoDiskANNTester
 
createPixelSet(float[][], int[][], String) - Static method in class stereodisk.StereoDiskROC
 
createRotation(int, int, float, Roi) - Method in class FlowJ.FlowJFlow
 
createSampleBlock(float[], int) - Static method in class stereodisk.StereoDiskAnalyzer
Create an unbalanced sample block.
createSampleBlock(float[], int) - Static method in class stereodisk.StereoDiskIxConverter
Kreeer een block van n x,y coordinaten waarmee de kans zo hoog mogelijk is om 1:1:1 van de 3 classificaties te vangen.
createSampleBlocks(float[][], int) - Static method in class stereodisk.StereoDiskAnalyzer
Create as many blocks of balanced pixel indices as there are images in images.
createSampleBlocks(float[][], int) - Static method in class stereodisk.StereoDiskIxConverter
Create as many blocks of balanced pixel indices as there are images in images.
createTestingCoords(float[][]) - Static method in class stereodisk.StereoDiskANNTester
 
createTestingCoords(float[][]) - Static method in class stereodisk.StereoDiskROC
 
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".
createTextField(Panel, String, String, int) - Method in class va.VAInterface
Create a text field with default content of length i (in characters).
CreateTextField(Panel, String, String, int) - Method in class bd.BDUserInterface
 
createTrainingCoords(float[][]) - Static method in class stereodisk.StereoDiskANNTester
 
createTrainingCoords(float[][]) - Static method in class stereodisk.StereoDiskROC
 
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
cropHeight - Static variable in class stereodisk.StereoDiskSlideCropper
 
cropLx - Static variable in class stereodisk.StereoDiskSlideCropper
 
cropLy - Static variable in class stereodisk.StereoDiskSlideCropper
 
cropRx - Static variable in class stereodisk.StereoDiskSlideCropper
 
cropRy - Static variable in class stereodisk.StereoDiskSlideCropper
 
cropWidth - Static variable in class stereodisk.StereoDiskSlideCropper
 
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
 
cycles - Variable in class registration.SearchMI
 
cycles(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the cycles of a given permutation, as int arrays.
cyclesFun(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the cycles of a given permutation understood as a function of the indices, as int arrays.
cyclesToString(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the Permutation.cycles(int[]) view of the permutation as a String.
cyclesToString(int[][]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the Permutation.cycles(int[]) view of the permutation as a String.

D

d - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer
 
D(float[], float[], int, double, float[], String) - Static method in class knn.StereoFilterBank
Calculate a depth map at the chosen scale.
dA(HyperVolume, int, int, int, int) - Static method in class volume.Diffusion3D
 
DanConverter - class retina.DanConverter.
Implements program for converting dan's data from tsolab to tiff.
DanConverter() - Constructor for class retina.DanConverter
 
DATA_EXTENSION - Static variable in class retina.OIDHeader
 
dataset - Variable in class bijnum.BIJknn
The dataset, a MxN matrix of N-dimensional vectors.
date - Variable in class retina.OIDHeader
 
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
 
DBrent - class numericalMethods.calculus.minimizing.DBrent.
 
DBrent() - Constructor for class numericalMethods.calculus.minimizing.DBrent
 
dc1 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
dc3 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
dc4 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
dc5 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
dc6 - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
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 - Static variable in class numericalMethods.calculus.minimizing.nmPowell
 
debug - Static variable in class numericalMethods.calculus.minimizing.ConjugateGradient
 
debug - Variable in class of3d.OF3DLucas
 
debug - Variable in class registration.RegisterFFTHessian
 
debug - Variable in class registration.RegisterFFT
 
DEBUG - Static variable in class numericalMethods.calculus.rootFinding.NewtonRaphson
Switches debug output on and off; the default is false.
decomposable(double[][]) - Static method in class numericalMethods.algebra.linear.decompose.Cholesky
Invokes Cholesky.decomposable(double [][], double ) with a tolerance of eps = 1e-14.
decomposable(double[][], double) - Static method in class numericalMethods.algebra.linear.decompose.Cholesky
Checks if A has a cholesky decomposition, which is, if A is symmetric and positive definite.
decompose(double[][]) - Static method in class numericalMethods.algebra.linear.decompose.LR
Decomposes a real matrix.
decompose(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.LR
Decomposes a complex matrix.
decompose(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.Cholesky
Computes the cholesky decomposition of matrix A and stores the result in L .
decompose(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.QR
Decomposes a real matrix.
decompose(double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.LR
Decomposes a real matrix.
decompose(double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.Householder
Decomposes a real matrix.
decompose(double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.QR
Decomposes a real matrix.
decompose(double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.QR
Decomposes a complex matrix.
decompose(double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.LR
Decomposes a complex matrix.
decompose(double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.Householder
Decomposes a complex matrix.
decompose(double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.QR
Decomposes a complex matrix.
decompose(double[][], double[][], double[][], double[][], double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.decompose.Householder
Decomposes a complex matrix while separating the orthogonal matrix.
decompose(double[][], double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.decompose.Householder
Decomposes a real matrix while separating the orthogonal matrix.
decompose(double[][], double[][], double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.decompose.Householder
Decomposes a complex matrix storing the result in a merged way.
decompose(double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.decompose.Householder
Decomposes a real matrix storing the result in a merged way.
decompose(int[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.PLR
Decomposes a real matrix.
decompose(int[][], double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.PLR
Decomposes a complex matrix.
decompose(int[], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.PLR
Decomposes a real matrix.
decompose(int[], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.PLR
Decomposes a complex matrix.
DEFAULTCOOLINGRATE - Static variable in class net.sourceforge.jannealer.AnnealingScheme
 
defaultDirectory - Static variable in class VolumeJ.VJUserInterface
 
defaultDirectory - Static variable in class bd.BDUserInterface
 
DEFAULTITERATIONS - Static variable in class net.sourceforge.jannealer.AnnealingScheme
 
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.
DEFAULTOLERANCE - Static variable in class net.sourceforge.jannealer.AnnealingScheme
 
DEFAULTTEMP - Static variable in class net.sourceforge.jannealer.AnnealingScheme
default temperature
defaultViewport() - Method in class VolumeJ.VJRenderer
Get a default viewport automatically.
Delaunay - class numericalMethods.geometry.meshGeneration.ruppert.Delaunay.
 
Delaunay(double[]) - Constructor for class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
Delaunay(double[][]) - Constructor for class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
DelaunayViewer - class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.
 
DelaunayViewer.DelaunayPanel - class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel.
 
DelaunayViewer.DelaunayPanel(DelaunayViewer, Ruppert, DelaunayViewer, DelaunayViewer.DrawingPanel) - Constructor for class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel
 
DelaunayViewer.DrawingPanel - class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DrawingPanel.
 
DelaunayViewer.DrawingPanel(DelaunayViewer) - Constructor for class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DrawingPanel
 
DelaunayViewer(int, Ruppert) - Constructor for class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer
 
DelaunayViewer(Ruppert) - Constructor for class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer
 
delete(String) - Method in class volume.VolumeIO
 
deleteObsoleteFaces() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
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
 
depth(float[], float[], int, String) - Method in class knn.StereoFilterBank
Compute a depth map.
derivative(double[], double[], int, int, double[], double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
computes the nth derivative of given polynomial.
derivative(double[], double[], int, int, int, double[], double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexLaurentPolynomial
computes the nth derivative of given polynomial.
derivChoice - Variable in class bd.BDUserInterface
 
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
 
DesignMatrix - class bijfit.DesignMatrix.
 
DesignMatrix() - Constructor for class bijfit.DesignMatrix
 
DesignMatrixExponential - class bijfit.DesignMatrixExponential.
Design Matrix for simple exponential, to be used in GeneralLeastSquares estimation.
DesignMatrixExponential(float[]) - Constructor for class bijfit.DesignMatrixExponential
Create a design matrix for the exponential function.
DesignMatrixGamma - class bijfit.DesignMatrixGamma.
Design Matrix for gamma variate model, to be used in GeneralLeastSquares estimation.
DesignMatrixGamma(float[], float, float) - Constructor for class bijfit.DesignMatrixGamma
Create a design matrix for the derived gamma variate function.
DesignMatrixLinear - class bijfit.DesignMatrixLinear.
Design Matrix for linear function, to be used in GeneralLeastSquares estimation.
DesignMatrixLinear(double[]) - Constructor for class bijfit.DesignMatrixLinear
Create a linear model design matrix.
DesignMatrixLinear(float[]) - Constructor for class bijfit.DesignMatrixLinear
Create a linear model design matrix.
DesignMatrixPoly - class bijfit.DesignMatrixPoly.
Design Matrix for polynomials, to be used in GeneralLeastSquares estimation.
DesignMatrixPoly(double[], int) - Constructor for class bijfit.DesignMatrixPoly
Create a polynomial model design matrix of the n'th order.
DesignMatrixPoly(int, int) - Constructor for class bijfit.DesignMatrixPoly
Create a polynomial design matrix from a sequence 1..k x's.
det - Static variable in class numericalMethods.geometry.latticeReduction.ExactLLL
 
DET - Static variable in class bd.BlobDetector
 
det() - Method in class Jama.Matrix
Matrix determinant
det() - Method in class Jama.LUDecomposition
Determinant
det(float[], int, double) - Static method in class volume.Hessian
Compute the determinant of the Hessian matrix of image.
detect - Variable in class bd.BDUserInterface
 
detect() - Method in class bd.BlobDetector
 
detect(VolumeFloat, double) - Method in class bd.BlobDetector
 
detectold(VolumeFloat, double) - Method in class bd.BlobDetector
 
Determinant - class numericalMethods.algebra.linear.Determinant.
Computes the determinant of a square matrix.
Determinant() - Constructor for class numericalMethods.algebra.linear.Determinant
 
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.
diagnosisLabel - Variable in class bd.BDUserInterface
 
dialog - Variable in class io.OpenPreviewDialog
 
dict - Variable in class retina.ScriptProcessor
 
diffPairwise(float[][], int, int, int) - Static method in class retina.OIDAnalysis
Perform pairwise differencing on all conditions.
diffPairwise(float[][], int, int, int) - Method in class retina.OIDStackWindow
Perform pairwise differencing on all conditions.
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
 
dim - Static variable in class numericalMethods.geometry.latticeReduction.LLL
 
direction - Variable in class numericalMethods.calculus.minimizing.nmLineND
 
directory - Static variable in class io.OpenPreviewDialog
 
directory - Variable in class retina.OIDHeader
 
directory - Variable in class retina.ScriptProcessor
The working directory from which you are analyzing, i.e.
directory - Variable in class retina.RTA_Thickness_Reader
 
directory - Static variable in class retina.EpochSorter
 
directory - Variable in class retina.RTA_Reader
 
directory - Static variable in class retina.DanConverter
 
directory - Static variable in class va.VAInterface
 
directoryResults - Static variable in class retina.ScriptProcessor
 
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
 
DISPLAY_SCALING - Static variable in class retina.ScriptProcessor
 
displayon - Variable in class FlowJ.FlowJLucas
 
displayon - Variable in class of3d.OF3DLucas
 
distance(double[]) - Method in interface net.sourceforge.jannealer.ObjectiveFunction
 
distance(double[]) - Method in class net.sourceforge.jannealer.test.InverseObjectiveFunction
 
distance(double, double, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
distance(double, double, int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
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.
distanceToCenterHorizontal(int, int) - Static method in class knn.FeatureComputer
Make a feature with the distance to the center of the image for each pixel.
distanceToCenterVertical(int, int) - Static method in class knn.FeatureComputer
Make a feature with the distance to the center of the image for each pixel.
DISTANCEXT - Static variable in class retina.ScriptProcessor
 
DISTANCEXVERTICAL - Static variable in class retina.ScriptProcessor
 
DISTANCEYHORIZONTAL - Static variable in class retina.ScriptProcessor
 
DISTANCEYT - Static variable in class retina.ScriptProcessor
 
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.
divide(double[][], double[][], double, double, double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs A / b = C.
divide(double[][], double, double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs A / b = C.
divide(double[], double[], double, double, double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector.
divide(double[], double[], int, double[], double[], int, double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
divide(double[], double, double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector a / b = c.
divide(double, double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs b / A = C.
divide(double, double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs b / (Are+i*Aim) = (Cre+i*Cim).
divide(double, double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector: a / b = c .
divide(double, double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector: a / (re+i*im) = (resRe+i*resIm) .
divide(double, int[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs b / A = C.
divide(double, int[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector: a / b = c .
divide(int[][], double, double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs A / b = C.
divide(int[][], int, int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs A / b = C.
divide(int[], double, double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
scales vector a /b = c.
divide(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
 
divide(int[], int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Puts p1 composed with Permutation.inverse(int[])(p2) into the third argument.
divide(int[], int, int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector.
divide(int, int[][], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs b / A = C.
divide(int, int[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector: a / b = c .
divideByX(double[]) - Static method in class numericalMethods.calculus.functionApproximation.ChebyshevApproximation
Called with coefficients c[j] of a Chebyshev series which sums to a function f(x) with f(0) = 0, returns with c holding the coefficients of the Chebyshev expansion of f(x)/x.
divideFun(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
 
divideFun(int[], int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Puts p1[p2^-1[i]] into the third argument.
DIVISION - Static variable in class retina.OIDProcessor
 
DIVISION - Static variable in class retina.OIDAnalysis
 
division(float[], float[], float[], float[]) - Static method in class retina.OIDroiAnalyzer
 
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[ ].
doAvg - Static variable in class retina.OIDReconstructor
 
doAvg - Variable in class retina.OIDProcessor
 
doBackface - Variable in class VolumeJ.VJShader
 
DocletDummy - class numericalMethods.DocletDummy.
 
DocletDummy - class numericalMethods.algebra.DocletDummy.
 
DocletDummy - class numericalMethods.calculus.DocletDummy.
 
DocletDummy - class numericalMethods.geometry.DocletDummy.
 
DocletDummy - class numericalMethods.geometry.meshGeneration.DocletDummy.
 
DocletDummy() - Constructor for class numericalMethods.DocletDummy
 
DocletDummy() - Constructor for class numericalMethods.algebra.DocletDummy
 
DocletDummy() - Constructor for class numericalMethods.calculus.DocletDummy
 
DocletDummy() - Constructor for class numericalMethods.geometry.DocletDummy
 
DocletDummy() - Constructor for class numericalMethods.geometry.meshGeneration.DocletDummy
 
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
 
doExecute - Variable in class retina.ScriptProcessor
 
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_scales - Static variable in class knn.FeatureComputer
 
dog_xshifts - Static variable in class knn.FeatureComputer
 
DoG(double) - Constructor for class volume.DoG
Create a Difference of Gaussian kernel from standard deviation sigma.
DOG(float[], float[], int, double, double, String) - Static method in class knn.DOGFilterBank
Compute a stereo difference image.
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
 
dogFilter - Static variable in class knn.FeatureComputer
 
DOGFilterBank - class knn.DOGFilterBank.
This class implements a dog difference of gaussians filterbank, i.e.
DOGFilterBank(float[], float[]) - Constructor for class knn.DOGFilterBank
 
doLast2 - Static variable in class retina.OIDReconstructor
 
doLinearCorrect - Static variable in class retina.OIDReconstructor
 
doLinearCorrect - Variable in class retina.OIDProcessor
 
doOnlyStim - Static variable in class retina.OIDReconstructor
 
doPerspective - Variable in class VolumeJ.VJRenderer
 
doPixeltracing - Variable in class VolumeJ.VJRenderer
Pixel tracing variables.
doPP - Variable in class retina.OIDTimecourseAnalyzer
 
doPsi() - Method in class of3d.OF3DUserInterface
 
doRegister - Static variable in class retina.OIDReconstructor
 
doRegistration - Variable in class retina.ScriptProcessor
 
doRegistration - Variable in class retina.OIDProcessor
 
doSmooth - Variable in class retina.OIDProcessor
 
doSubOpp - Static variable in class retina.OIDReconstructor
 
doSubOpp - Variable in class retina.OIDProcessor
 
dot(double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs dot product
doubleArea - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
doubleArrayParameter - Variable in class numericalMethods.calculus.minimizing.NumericalGradient
 
doubleArrayParametrized - Variable in class numericalMethods.calculus.minimizing.nmLineNDEvaluator
 
DoubleArrayValueCacher - class numericalMethods.function.util.DoubleArrayValueCacher.
 
DoubleArrayValueCacher(DoubleParametrized, DoubleArrayValued) - Constructor for class numericalMethods.function.util.DoubleArrayValueCacher
 
DoubleArrayValueCacher(int) - Constructor for class numericalMethods.function.util.DoubleArrayValueCacher
 
doubleArrayValued - Variable in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
doubleArrayValued - Variable in class numericalMethods.calculus.minimizing.LineNDDBrent
 
doubleArrayValued - Variable in class numericalMethods.function.util.DoubleArrayValueCacher
 
DoubleArrayValuedIntegrator - interface numericalMethods.calculus.integration.DoubleArrayValuedIntegrator.
 
doubleArrayValueLength - Variable in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
doubleArrayValueLength - Variable in class numericalMethods.function.util.AbstractValueCacher
 
doubleMaxArea - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
doubleParametrized - Variable in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
doubleParametrized - Variable in class numericalMethods.function.util.AbstractValueCacher
 
doubleSize(boolean[]) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
doubleSize(double[]) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
doubleSize(int[]) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
DoubleValueCacher - class numericalMethods.function.util.DoubleValueCacher.
 
DoubleValueCacher() - Constructor for class numericalMethods.function.util.DoubleValueCacher
 
DoubleValueCacher(DoubleParametrized, DoubleValued) - Constructor for class numericalMethods.function.util.DoubleValueCacher
 
doubleValued - Variable in class numericalMethods.calculus.minimizing.nmLineNDEvaluator
 
doubleValued - Variable in class numericalMethods.function.util.DoubleValueCacher
 
drawCenter(ImageProcessor) - Method in class registration.LocatedCircle
Draws the center on an ImageProcessor.
drawLine(ImageProcessor, String, int) - Method in class retina.OIDWindow
 
drawOutline(ImagePlus) - Method in class registration.LocatedCircle
Returns a circle containing the circumference as a Roi.
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 - Variable in class bijnum.BIJfft
 
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
 
eatExterior() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
eatExterior(double[][]) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
eatFace(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
edge - Variable in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
edge - Variable in class volume.Volume
 
edge(int, int, int) - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
edgeIllegal(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
edgeIllegal(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
edgeInFace(int, int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
effectDragging(int, int) - Method in class VolumeJ.VJViewerCanvas
User pressed mouse button, moved mouse, and released.
eig() - Method in class Jama.Matrix
Eigenvalue Decomposition
eigenimages - Variable in class bijnum.BIJpca
The matrix of eigenimages, i.e.
EigenvalueDecomposition - class Jama.EigenvalueDecomposition.
Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(Matrix) - Constructor for class Jama.EigenvalueDecomposition
Check for symmetry, then construct the eigenvalue decomposition
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
 
encroached(int, double, double) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
encroached(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
encroached(int, int, double, double) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
end - Static variable in class retina.OIDReconstructor
 
end - Variable in class retina.OIDProcessor
Other parameters describing the layout of aggregate.
END - Static variable in class retina.ScriptProcessor
The last frame at which the stimulus was on, or the end of the stimulus timecourse.
endx - Variable in class of3d.OF3DDeformer
 
endy - Variable in class of3d.OF3DDeformer
 
endz - Variable in class of3d.OF3DDeformer
 
epochNames - Variable in class retina.OIDProcessor
 
EpochSorter - class retina.EpochSorter.
Sets the condition text in the OID .kes file to reflect the stimulus condition given by the a script.
EpochSorter() - Constructor for class retina.EpochSorter
 
eps - Variable in class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
eps - Variable in class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
eps - Variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
eps - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
eps - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer
 
eps - Variable in class numericalMethods.function.util.AbstractValueCacher
 
EPS - Static variable in class numericalMethods.calculus.minimizing.ConjugateGradient
 
EPS - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
EPS - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
EPS - Static variable in class numericalMethods.calculus.specialFunctions.TestClausen
 
EPS - Static variable in class numericalMethods.geometry.bounding.BoundingBox
 
epsilon - Static variable in class stereodisk.StereoDiskANNTester
 
epsilon - Static variable in class stereodisk.StereoDiskROC
 
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.
err - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer
 
ERRCON - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
ERRCON - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
error(String) - Static method in class FlowJ.FlowJUserInterface
 
error(String) - Static method in class VolumeJ.VJUserInterface
Writes a string to an error channel.
estimate - Variable in class registration.Register
The estimate of the registration parameters.
estimate(float[][], float[], int, int, double) - Static method in class knn.ANN
Determine the ANN classification for an array of feature vectors.
eulerSum(double[]) - Static method in class numericalMethods.calculus.integration.NewtonCotes
 
eval(double[], double[], int, double, double, double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
evaluates the polynomial a with the coefficients a_k = aRe[k] + i aIm[k] and degree degOfA at z = x + i y and returns the result in aAtZ.
eval(double[], double[], int, int, double, double, double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
evaluates the polynomial a with the coefficients a_k = aRe[k + offsetOfA ] + i aIm[k + offsetOfA] and degree degOfA at z = x + i y and returns the result in aAtZ.
eval(double[], double[], int, int, double, double, double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexLaurentPolynomial
evaluates the polynomial a with the coefficients a_k = aRe[k] + i aIm[k] and degree degOfA at z = x + i y and returns the result in aAtZ.
evalDerivative(double[], double[], int, int, double, double, double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
evaluates the n-the derivative of the polynomial a with the coefficients a_k = aRe[k + offsetOfA ] + i aIm[k + offsetOfA] and degree degOfA at z = x + i y and returns the result in dAAtZ.
evalDerivative(double[], double[], int, int, int, double, double, double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
evaluates the n-the derivative of the polynomial a with the coefficients a_k = aRe[k + offsetOfA ] + i aIm[k + offsetOfA] and degree degOfA at z = x + i y and returns the result in dAAtZ.
evalDerivative(double[], double[], int, int, int, double, double, double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexLaurentPolynomial
evaluates the n-the derivative of the polynomial a with the coefficients a_k = aRe[k + offsetOfA ] + i aIm[k + offsetOfA] and degree degOfA at z = x + i y and returns the result in dAAtZ.
evals - Variable in class numericalMethods.calculus.minimizing.Sin
 
evals - Variable in class numericalMethods.calculus.minimizing.Cos
 
evaluate(double[], double) - Static method in class numericalMethods.calculus.functionApproximation.ChebyshevApproximation
Evaluates the Chebyshev series with coefficients cj.
ExactLLL - class numericalMethods.geometry.latticeReduction.ExactLLL.
 
ExactLLL() - Constructor for class numericalMethods.geometry.latticeReduction.ExactLLL
 
Example1D - class numericalMethods.calculus.minimizing.Example1D.
 
Example1D() - Constructor for class numericalMethods.calculus.minimizing.Example1D
 
ExampleIntegration - class numericalMethods.calculus.integration.ExampleIntegration.
This classs illustrates the usage of the numerical integrators, which are based on adaptive ode solvers.
ExampleIntegration.F - class numericalMethods.calculus.integration.ExampleIntegration.F.
In numericalMethods funtions are defined by a pair of interfaces describing parameter and value space seperatly.
ExampleIntegration.F() - Constructor for class numericalMethods.calculus.integration.ExampleIntegration.F
 
ExampleIntegration() - Constructor for class numericalMethods.calculus.integration.ExampleIntegration
 
ExampleND - class numericalMethods.calculus.minimizing.ExampleND.
 
ExampleND() - Constructor for class numericalMethods.calculus.minimizing.ExampleND
 
ExampleNewtonRaphson - class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.
 
ExampleNewtonRaphson.ComplexSinus - class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.ComplexSinus.
 
ExampleNewtonRaphson.ComplexSinus() - Constructor for class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.ComplexSinus
 
ExampleNewtonRaphson.RealSinus - class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.RealSinus.
 
ExampleNewtonRaphson.RealSinus() - Constructor for class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.RealSinus
 
ExampleNewtonRaphson() - Constructor for class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson
 
ExampleODE - class numericalMethods.calculus.odeSolving.ExampleODE.
This classs illustrates the usage of the ode solvers.
ExampleODE.F - class numericalMethods.calculus.odeSolving.ExampleODE.F.
In numericalMethods funtions are defined by a pair of interfaces describing parameter and value space seperatly.
ExampleODE.F() - Constructor for class numericalMethods.calculus.odeSolving.ExampleODE.F
 
ExampleODE() - Constructor for class numericalMethods.calculus.odeSolving.ExampleODE
 
exit(int, int, int, String, String) - Method in class retina.OIDAnalyzer
Hook for exit.
exit(int, int, int, String, String) - Method in class retina.OIDTimecourseAnalyzer
Hook for exit.
exit(int, int, int, String, String) - Method in class retina.OIDMapsFitter
 
exit(int, int, int, String, String) - Method in class retina.OIDroiAnalyzer
 
exit(int, int, int, String, String) - Method in class retina.OIDPCAAnalyzer
Hook for exit.
exit(int, int, int, String, String) - Method in class retina.OIDROItimecourseAnalyzer
Hook for exit.
exit(int, int, int, String, String) - Method in interface retina.OIDBaseAnalyzer
 
exit(int, int, int, String, String) - Method in class retina.OIDAverageAnalyzer
Hook for exit.
extend(double[]) - Static method in class bijnum.BIJfft
 
extend(float[]) - Static method in class bijnum.BIJfft
 
extract(float[], int, int, int, int, int) - Static method in class volume.Transformer
Extract a new float [] image from an image.
extraInfo - Variable in class retina.OIDHeader
 
Extrap - class numericalMethods.calculus.odeSolving.Extrap.
A program for numerical solution of a system of first order ordinary differential equations y' = f( x, y).
It uses an Extrapolation-Algorithm (GBS), based on the explicit midpoint rule (with stepsize control, order selection).

This method is described in Section II.9 of the book:
E.
Extrap() - Constructor for class numericalMethods.calculus.odeSolving.Extrap
 
Extrap(int) - Constructor for class numericalMethods.calculus.odeSolving.Extrap
 
Extrap(int, int) - Constructor for class numericalMethods.calculus.odeSolving.Extrap
 
ExtrapIntegrator - class numericalMethods.calculus.integration.ExtrapIntegrator.
 
ExtrapIntegrator() - Constructor for class numericalMethods.calculus.integration.ExtrapIntegrator
 
ExtrapIntegrator(DoubleParametrized, DoubleArrayValued) - Constructor for class numericalMethods.calculus.integration.ExtrapIntegrator
 
ExtrapIntegrator(DoubleParametrized, DoubleArrayValued, boolean) - Constructor for class numericalMethods.calculus.integration.ExtrapIntegrator
 
ExtrapIntegrator(int) - Constructor for class numericalMethods.calculus.integration.ExtrapIntegrator
 
ExtrapIntegrator(int, boolean) - Constructor for class numericalMethods.calculus.integration.ExtrapIntegrator
 

F

f - Variable in class numericalMethods.calculus.minimizing.NumericalGradient
 
f - Static variable in class numericalMethods.calculus.minimizing.LineNDDBrent
 
f - Static variable in class numericalMethods.calculus.minimizing.nmLineNDBrent
 
F - Variable in class numericalMethods.calculus.minimizing.NumericalGradient
 
face - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer
 
face - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
factor(double[][][], double[][][], double[][][], double[][][], double[][][], double[][][], double[][], double[][], double[], double[], double[], double[], double[][], double[][], double[][], double[][], double[][], double[][], double[][][], double[][][], double[], double[], int, int, int) - Static method in class numericalMethods.algebra.loopGroup.BirkhoffFactorization
 
factor(double[][][], double[][][], double[][][], double[][][], double[][], double[][], double[], double[], double[], double[], double[][], double[][], double[][], double[][], int) - Static method in class numericalMethods.algebra.loopGroup.IwasawaFactorization
Compute Iwasawa factorization.
factor(double[][][], double[][][], double[][][], double[][][], int) - Static method in class numericalMethods.algebra.loopGroup.IwasawaFactorization
Compute Iwasawa factorization Input: (xRe, xIm), R Output: (fRe, fIm)
factor(double[][][], double[][][], double[][][], double[][][], int, int, int) - Static method in class numericalMethods.algebra.loopGroup.BirkhoffFactorization
Computes one of the factors of a Birkhoff factorization of a GL_n(C)-valued loop X.
factorial(int) - Static method in class numericalMethods.algebra.group.Permutation
factorial(n)=n!=n*(n-1)*...*1.
fDirectory - Static variable in class stereodisk.StereoDiskFeatureConverter
 
Feature - class knn.Feature.
Feature defines a feature vector, which is a float[] vector and some other characteristics to make it a feature vector.
Feature(String, byte[]) - Constructor for class knn.Feature
 
Feature(String, float[]) - Constructor for class knn.Feature
 
featureBlobs(float[], int) - Static method in class registration.RegisterRetina
 
FeatureComputer - class knn.FeatureComputer.
FeatureComputer computes a feature for an image.
FeatureComputer() - Constructor for class knn.FeatureComputer
 
featureEdges(float[], int) - Static method in class registration.RegisterRetina
 
FeatureJ.src - package FeatureJ.src
 
featureNamePrefix(int) - Static method in class knn.FeatureComputer
make a String that is the prefix for all feature files.
Features - class knn.Features.
Features defines a collection of features.
Features() - Constructor for class knn.Features
 
Features(float[][], int, String) - Constructor for class knn.Features
 
fexp(double) - Method in class bijfit.DesignMatrixExponential
Return a double[] vector containing the basis functions at x.
ff - Variable in class retina.OIDAverageAnalyzer
 
ffavg - Variable in class retina.OIDAverageAnalyzer
 
fgamma(float, float, float) - Method in class bijfit.DesignMatrixGamma
Return a double[] vector containing the basis functions at x for a derived gamma variate.
fht - Variable in class registration.RegisterFFTHessian
to compute FFT.
fht - Variable in class registration.RegisterFFT
to compute FFT.
fhtps(int, int, float[], float[]) - Method in class bijnum.BIJfht
Calculate the Power Spectrum of one row from 2D Hartley Transform.
fi - Variable in class retina.OIDProcessor
 
fieldEnd - Variable in class retina.PCAWindow
 
fieldEnd - Variable in class retina.OIDReconstructor
 
fieldGaussian - Variable in class retina.OIDReconstructor
 
fieldScaling - Variable in class retina.OIDReconstructor
 
fieldStart - Variable in class retina.PCAWindow
 
fieldStart - Variable in class retina.OIDReconstructor
 
file - Variable in class io.FileAndString
 
FileAndString - class io.FileAndString.
Utility class for OpenPreviewDialog
FileAndString(File, String) - Constructor for class io.FileAndString
 
fileControlFile - Static variable in class retina.EpochSorter
 
fileName - Variable in class retina.OIDHeader
 
FilenameFilterAcceptOID - class retina.FilenameFilterAcceptOID.
Defines a FilenameFilter for KES OID files, for any Java version.
FilenameFilterAcceptOID() - Constructor for class retina.FilenameFilterAcceptOID
 
filesDirectory - Variable in class retina.ScriptProcessor
The directory where the sequence files are located.
fill(double[], double) - Static method in class numericalMethods.util.Arrays
Fills target with value.
fill(double[], double[]) - Static method in class numericalMethods.util.TupleSequences
Fills target with value.
fill(double[], int, double) - Static method in class numericalMethods.util.TupleSequences
Fills target with value.
fill(double[], int, int, double) - Static method in class numericalMethods.util.Arrays
Fills target from postion to postion+length-1 with value.
fill(float[], float) - Static method in class numericalMethods.util.Arrays
Fills target with value.
fill(float[], int, int, float) - Static method in class numericalMethods.util.Arrays
Fills target from postion to postion+length-1 with value.
fill(int[], int) - Static method in class numericalMethods.util.Arrays
Fills target with value.
fill(int[], int, int, int) - Static method in class numericalMethods.util.Arrays
Fills target from postion to postion+length-1 with value.
filter - Variable in class io.OpenPreviewDialog
 
filter(float[], int, float[]) - Static method in class knn.FilterBank
Convolve image with a filter bank with 0,1 and 2nd order oriented derivative of Gaussian filter (Gabor wavelets) at a number of scales and orientations.
filter(float[], int, int) - Static method in class stereodisk.StereoDiskPGMToFeatureConverter
Filter a depth map original.
filter(int, float[], float[], int, String) - Method in class knn.StereoFilterBank
Apply the filter to a stereo pair.
filter(int, float[], float[], int, String) - Method in class knn.DOGFilterBank
Apply the filter to a stereo pair.
filter(int, float[], int, String) - Method in class knn.FilterBank
Apply the next filter to an image.
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.
filterBank - Static variable in class knn.FeatureComputer
 
FilterBank - class knn.FilterBank.
This class implements a filterbank, i.e.
FilterBank(float[], int) - Constructor for class knn.FilterBank
 
finalize() - Method in class numericalMethods.function.util.AbstractValueCacher
 
find(float[]) - Static method in class bijfit.Maximum
Find the index of the maximum in a vector.
find(float[], int) - Static method in class bijfit.Maximum
Find the integer position of the maximum in an image of width pixels, i.e.
findBestFeature(Features, float[], Features, float[], int, int, int[]) - Static method in class stereodisk.StereoCupRimClassifier
Find the feature that gives the highest incremental accuracy gain.
findFOV(float[], int, boolean) - Static method in class retina.RetinalImage
 
findFOV(float[], int, boolean, double) - Static method in class retina.RetinalImage
Locate the circular FOV (the boundary of the actual retina in the image).
findMaxPositionFromCorner(float[], int, int, int[], int, int) - Static method in class retina.RetinalImage
Find the location of the pixel with the maximum value on the line starting at x,y and stepping by xstep, ystep.
findSubpixel(float[], int) - Static method in class bijfit.Maximum
Find the location of the maximum value in image relative to the center of the image at 0,0) with subpixel accuracy by fitting a quadratic curve to the peak.
findThresholdPositionFromCorner(float[], int, int, int[], int, int, float) - Static method in class retina.RetinalImage
Find the location of the first pixel with a value equal or higher than treshold on the line starting at x,y and stepping by xstep, ystep.
findTriangle(double, double) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
FINETHRESHOLD - Static variable in class VolumeJ.VJViewerCanvas
 
firePropertyChange(String) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
firePropertyChange(String) - Method in class numericalMethods.calculus.odeSolving.RungeKutta
 
firePropertyChange(String) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
firePropertyChange(String) - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
firePropertyChange(String) - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
firePropertyChange(String, Object, Object) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
firePropertyChange(String, Object, Object) - Method in class numericalMethods.calculus.odeSolving.RungeKutta
 
firePropertyChange(String, Object, Object) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
firePropertyChange(String, Object, Object) - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
firePropertyChange(String, Object, Object) - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
first - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer
 
FIRST - Static variable in class numericalMethods.algebra.loopGroup.BirkhoffFactorization
 
firstDerangement(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Let the parameter be the firstDerangement (permutation without fixed point) in the lexicographic order.
firstDiv - Variable in class retina.OIDWindow
 
firstFrame(ImageStack, float, int) - Static method in class FlowJ.FlowJLucas
Return the first frame for which you can compute the flow.
firstframeAnalysis(float[][], float[][], float[][], int, int, int, int, int) - Static method in class retina.OIDAnalysis
Do first frame analysis on each stimulus frame (averaged for each condition) in a separately.
firstframeAnalysisAllFrames(float[][], float[][], int, int, int, int, int, int, int, int) - Static method in class retina.OIDAnalysis
Do first frame analysis on all frames (averaged for each condition) in a separately, including the frames which were before the stimulus.
firstframeAnalysisDynamics(float[][], int, int, int, int, int, int, int) - Static method in class retina.OIDAnalysis
Make a dynamic movie of the first frame method.
firstframeConditionAnalysis(float[][], int, int, int, int) - Static method in class retina.OIDAnalysis
Do first frame analysis on each condition in a separately.
firstFrameDescription - Variable in class retina.OIDProcessor
 
firstframeDivisionCompact(float[][], int, int, int, int, int, int) - Static method in class retina.OIDAnalysis
Do first frame analysis on each stimulus frame (averaged for each condition) very compactly and in place.
firstframeDivisionDouble(float[][], float[][], float[][], int, int, int, int, int, int, int) - Static method in class retina.OIDAnalysis
Do first frame analysis on each stimulus frame (averaged for each condition) in a separately using double.
firstInCach - Variable in class numericalMethods.function.util.AbstractValueCacher
 
firstKey - Variable in class numericalMethods.function.util.AbstractValueCacher
 
firstname - Variable in class retina.OIDHeader
 
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(double[], DesignMatrix) - Static method in class bijfit.GeneralLinearLeastSquares
General least squares fit (with design matrix dm) to vector b.
fit(double[], DoubleParametrized, DoubleValued) - Static method in class numericalMethods.calculus.functionApproximation.ChebyshevApproximation
Calculates the coefficients cj, with n = c.length, for the function implemented by p and v.
fit(float[][], DesignMatrix) - Static method in class bijfit.GeneralLinearLeastSquares
General least squares fit (with design matrix dm) to a matrix of vectors b.
fit(float[], DesignMatrix) - Static method in class bijfit.GeneralLinearLeastSquares
General least squares fit (with design matrix dm) to vector b.
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.
fitAnalysis(float[][][], int, double, String, int) - Static method in class retina.OIDAnalysis
Determine the fit of the curve in
flatten(float[][]) - Static method in class bijnum.BIJmatrix
Flatten a float[][] matrix into a float[] matrix of rows each of m[0].width.
flipEdge(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
flipEdge(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
flipLR(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Flips the permutation left-right.
flipquad(float[]) - Method in class bijnum.BIJfht
Flip quadrants 1 and 3 and quadrants 2 and 4 of an image column vector.
flipUD(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Flips the permutation up-down.
FloatArrayParametrized - interface numericalMethods.function.FloatArrayParametrized.
Interface for objects that represent functions of a float array parameter.
FloatArrayValued - interface numericalMethods.function.FloatArrayValued.
Interface for objects that represent float array valued functions.
FloatParametrized - interface numericalMethods.function.FloatParametrized.
Interface for objects that represent functions of a float parameter.
floatvalue - Variable in class VolumeJ.VJValue
 
FloatValued - interface numericalMethods.function.FloatValued.
Interface for objects that represent float valued functions.
floor(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Floors matrix A and stores result in B.
floor(double[][], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Floors matrix A and stores result in B.
floor(double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Rounds vector a and stores result in b .
floor(double[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Rounds vector a and stores result in b .
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
 
fluctuate(int, double, long) - Method in class net.sourceforge.jannealer.Schedule
Description of the Method
fov - Variable in class retina.OIDWindow
Number of standarddeviations from average eye-motion to qualify as abnormal or blink.
FPCD - Static variable in class bd.BlobDetector
 
fpoly(double, int) - Method in class bijfit.DesignMatrixPoly
Return a double[] vector containing the basis function at x for a polynomial of order n-1.
fraction - Variable in class of3d.OFClassifierScintillans
 
fractionMagnitude - Variable in class VolumeJ.VJClassifierLevoy
 
frameBag - Variable in class va.VAInterface
 
frameCurrent - Variable in class va.TimedAcquisition
 
frameHeight - Variable in class retina.ScriptProcessor
 
FRAMEHEIGHT - Static variable in class retina.ScriptProcessor
 
frameNumber - Variable in class va.VAInterface
 
frames - Variable in class va.TimedAcquisition
 
frames - Variable in class va.ThreadCompression
 
framesPhase1 - Variable in class va.TimedAcquisition
 
framesTimestamps - Variable in class va.TimedAcquisition
 
framesTimestamps - Variable in class va.ThreadCompression
 
framesToStack(String, short[][]) - Method in class va.TimedAcquisition
 
frameWidth - Variable in class retina.ScriptProcessor
 
FRAMEWIDTH - Static variable in class retina.ScriptProcessor
 
freeUnusedKeys() - Method in class numericalMethods.function.util.AbstractValueCacher
 
fromCycles(int[][]) - Static method in class numericalMethods.algebra.group.Permutation
Returns a permutation built from its cycles.
fromCycles(int[][], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Changes result to a permutation of the same length, built from the given cycles.
fromCyclesFun(int[][], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Changes result to a permutation of the same length, built from the given cycles, as a function of the indices.
fromInversions(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the permutation having inv as its inversions vector.
fromInversions(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the permutation having inv as its inversions vector.
fromInversionsFun(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the permutation, in functional notation, having inv as its inversions vector.
fromInversionsFun(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the permutation, in functional notation, having inv as its inversions vector.
fromYoungTableaux(int[][][]) - Static method in class numericalMethods.algebra.group.Permutation
Gives the pair of int[][] Young tableaux associated with the int[] permutation.
full - Variable in class FlowJ.FlowJFlow
 
full(int, int) - Method in class FlowJ.FlowJFlow
 
fullfieldAnalysis(float[][], float[][], int, int, int, int) - Static method in class retina.OIDAnalysis
Analysis without masks.
function - Variable in class net.sourceforge.jannealer.AnnealingScheme
 
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.
functionName - Static variable in class retina.OIDAnalyzer
 
functionName - Static variable in class retina.OIDMapsFitter
 
functionName - Static variable in class retina.OIDroiAnalyzer
 
functionName - Static variable in class retina.OIDPCAAnalyzer
 
functionName - Static variable in class retina.OIDROItimecourseAnalyzer
 
FX_SIZE - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer
 
FY_SIZE - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer
 

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.
GAUSSIANDERIV - Static variable in class bd.BlobDetector
 
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
 
gcd(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Computes the greatest common divisor of several numbers.
gcd(int, int) - Static method in class numericalMethods.algebra.group.Permutation
Computes the greatest common divisor of two numbers.
gcomposite - Static variable in class FlowJ.FlowJSpotNoise
 
ge - Static variable in class FlowJ.FlowJSpotNoise
 
GeneralLinearLeastSquares - class bijfit.GeneralLinearLeastSquares.
 
GeneralLinearLeastSquares() - Constructor for class bijfit.GeneralLinearLeastSquares
 
get() - Method in class VolumeJ.VJValue
 
get() - Method in class VolumeJ.VJShade
 
get(int) - Method in class VolumeJ.VJShade
 
get(int) - Method in class retina.ScriptProcessor
 
get(int, int) - Method in class FlowJ.FlowJFlow
 
get(int, int) - Method in class Jama.Matrix
Get a single element.
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.
get(String) - Method in class retina.ScriptProcessor
 
getA() - Method in class VolumeJ.VJPlane
Get the A for the plane equation Ax+By+C+D=0 of this plane
getAbsoluteMinimumMI() - Method in class registration.SearchMI
Return the absolute minimal MI found along the search.
getAbsoluteMinimumParameters() - Method in class registration.SearchMI
Return the parameters corresponding to the absolute minimal MI found along the search.
getAbsTol() - Method in class numericalMethods.calculus.integration.ExtrapIntegrator
 
getAbsTol() - Method in class numericalMethods.calculus.odeSolving.Extrap
 
getAlpha() - Method in class VolumeJ.VJAlphaColor
 
getAlpha(int, int) - Method in class of3d.OF3DSpot
 
getAlphaDeg(int, int) - Method in class FlowJ.FlowJFlow
 
getAnalyzeStart() - Method in class retina.ScriptProcessor
 
getAngleConstraint() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
getAreaConstraint() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
getArray() - Method in class Jama.Matrix
Access the internal two-dimensional array.
getArrayCopy() - Method in class Jama.Matrix
Copy the internal two-dimensional array.
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
 
getBasename(String) - Static method in class stereodisk.StereoDiskConventions
Get the name of the original file that was observed for name.
getBasenames(String) - Static method in class stereodisk.StereoDiskConventions
Return a list of all unique basenames in directory.
getBasenamesFromFile(String, String) - Static method in class stereodisk.StereoDiskConventions
Return a list of basenames coming from a file in TEXT format.
getBaseNoExtension(String) - Static method in class stereodisk.StereoDiskConventions
Get the name of the original file that was observed for name,.
getBins() - Method in class bijnum.BIJmi
 
getBlue() - Method in class VolumeJ.VJAlphaColor
 
getBound() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
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
getCachValues() - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
getCenter() - Method in class registration.HoughTransform
Get the center of the first Hough transform circle.
getCircle(float[], int, int, float) - Method in class registration.HoughTransform
Find the circle in the image of radius.
getCircleCentersImageProcessor(ImagePlus, Vector) - Method in class registration.LocatedCircle
Make an overlay over an image imp indicating all the centers anf the circles.
getCircles(int, double) - Method in class registration.HoughTransform
Find the centers of the circles corresponding to radius by analyzing, but not within scale pixels of each other, the Hough transform for its maxima.
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
 
getCol(double[][], double[], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the column of matrix A in vector v.
getCol(int[][], int[], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns the column of matrix A in vector v.
getColumn(int) - Method in class VolumeJ.VJMatrix
Return the n-th column of the 3D transform matrix as a vector.
getColumnDimension() - Method in class Jama.Matrix
Get column dimension.
getColumnPackedCopy() - Method in class Jama.Matrix
Make a one-dimensional column packed copy of the internal array.
getComponent(double[], int, int, int) - Static method in class numericalMethods.util.TupleSequences
Returns a component of a tuple.
getCondStrings() - Method in class retina.ScriptProcessor
 
getConfidence() - Method in class registration.LocatedCircle
 
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.
getCoordinatesImageProcessor(int) - Method in class retina.PCAWindow
Create a plot (as ImageProcessor) of the j'th PCA coordinates.
getCurrentStepSize() - Method in class numericalMethods.calculus.odeSolving.Extrap
 
getD() - Method in class Jama.EigenvalueDecomposition
Return the block diagonal eigenvalue matrix
getD() - Method in class VolumeJ.VJPlane
Get the D for the plane equation Ax+By+C+D=0 of this plane
getDataFileName(String) - Static method in class retina.OIDHeader
From a file name, either header or data file, get the data file name (ending in _Data.kes).
getDate() - Method in class retina.OIDHeader
 
getDebug() - Static method in class numericalMethods.calculus.minimizing.nmPowell
Get the value of debug.
getDebug() - Static method in class numericalMethods.calculus.minimizing.ConjugateGradient
Get the value of debug.
getDefaultWindowSize() - Static method in class volume.Equalize
 
getDepth() - Method in class volume.Volume
 
getDiagonal(double[][], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Stores the diagonal of matrix A to v.
getDiagonal(int[][], int[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Stores the diagonal of matrix A to v.
getDiffuse() - Method in class VolumeJ.VJLight
 
getDimensions() - Method in class VolumeJ.VJGradient
 
getDirection() - Method in class numericalMethods.calculus.minimizing.nmLineND
Get the value of direction.
getDirectory() - Method in class io.OpenPreviewDialog
 
getDirectory() - Method in class retina.ScriptProcessor
 
getDoubleArrayParameterLength() - Method in class numericalMethods.calculus.minimizing.NumericalGradient
 
getDoubleArrayParameterLength() - Method in class numericalMethods.calculus.minimizing.Quadric
 
getDoubleArrayParameterLength() - Method in class numericalMethods.calculus.odeSolving.ExampleODE.F
 
getDoubleArrayParameterLength() - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.ComplexSinus
 
getDoubleArrayParameterLength() - Method in interface numericalMethods.function.nmDoubleArrayParametrized
Get the length of the double array parameter.
getDoubleArrayParameterLength() - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
getDoubleArrayParameterLength() - Method in class registration.SearchMI
 
getDoubleArrayValue() - Method in class numericalMethods.calculus.minimizing.NumericalGradient
 
getDoubleArrayValue() - Method in class numericalMethods.calculus.minimizing.nmLineND
 
getDoubleArrayValue() - Method in class numericalMethods.calculus.minimizing.Quadric
 
getDoubleArrayValue() - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.RealSinus
 
getDoubleArrayValue() - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.ComplexSinus
 
getDoubleArrayValue() - Method in class numericalMethods.function.util.DoubleArrayValueCacher
 
getDoubleArrayValue(double[], int) - Method in class numericalMethods.calculus.integration.ExampleIntegration.F
Queries function value.
getDoubleArrayValue(double[], int) - Method in class numericalMethods.calculus.minimizing.NumericalGradient
 
getDoubleArrayValue(double[], int) - Method in class numericalMethods.calculus.minimizing.nmLineND
 
getDoubleArrayValue(double[], int) - Method in class numericalMethods.calculus.minimizing.Quadric
 
getDoubleArrayValue(double[], int) - Method in class numericalMethods.calculus.odeSolving.ExampleODE.F
Queries derivatives.
getDoubleArrayValue(double[], int) - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.RealSinus
 
getDoubleArrayValue(double[], int) - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.ComplexSinus
 
getDoubleArrayValue(double[], int) - Method in interface numericalMethods.function.nmDoubleArrayValued
Writes the double array value into a double[].
getDoubleArrayValue(double[], int) - Method in class numericalMethods.function.util.DoubleArrayValueCacher
 
getDoubleArrayValue(double[], int) - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
getDoubleArrayValueLength() - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
getDoubleArrayValueLength() - Method in class numericalMethods.calculus.integration.ExampleIntegration.F
 
getDoubleArrayValueLength() - Method in interface numericalMethods.calculus.integration.DoubleArrayValuedIntegrator
 
getDoubleArrayValueLength() - Method in class numericalMethods.calculus.minimizing.NumericalGradient
 
getDoubleArrayValueLength() - Method in class numericalMethods.calculus.minimizing.nmLineND
 
getDoubleArrayValueLength() - Method in class numericalMethods.calculus.minimizing.Quadric
 
getDoubleArrayValueLength() - Method in class numericalMethods.calculus.odeSolving.ExampleODE.F
 
getDoubleArrayValueLength() - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.RealSinus
 
getDoubleArrayValueLength() - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.ComplexSinus
 
getDoubleArrayValueLength() - Method in interface numericalMethods.function.nmDoubleArrayValued
Get the length of the double array value.
getDoubleArrayValueLength() - Method in class numericalMethods.function.util.DoubleArrayValueCacher
 
getDoubleArrayValueLength() - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
getDoubleField(TextField) - Method in class bd.BDUserInterface
 
getDoubleField(TextField) - Method in class retina.PCAWindow
 
getDoublePivot() - Method in class Jama.LUDecomposition
Return pivot permutation vector as a one-dimensional double array
getDoubleValue() - Method in class numericalMethods.calculus.minimizing.NumericalGradient
 
getDoubleValue() - Method in class numericalMethods.calculus.minimizing.nmLineNDEvaluator
 
getDoubleValue() - Method in class numericalMethods.calculus.minimizing.LineNDDBrent.projectedGradient
 
getDoubleValue() - Method in class numericalMethods.calculus.minimizing.Quadric
 
getDoubleValue() - Method in class numericalMethods.calculus.minimizing.Sin
 
getDoubleValue() - Method in class numericalMethods.calculus.minimizing.Cos
 
getDoubleValue() - Method in interface numericalMethods.function.nmDoubleValued
Get the double value.
getDoubleValue() - Method in class numericalMethods.function.util.DoubleValueCacher
 
getDoubleValue() - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
getDoubleValue() - Method in class registration.SearchMI
Required because this class implements nmDoubleValued.
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.
getEps() - Method in class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
getEps() - Method in class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
getEps() - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
getEps() - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
getEps() - Method in class numericalMethods.function.util.AbstractValueCacher
 
getFeaturenames(String) - Static method in class stereodisk.StereoDiskConventions
Return a list of all feature files in directory.
getFile() - Method in class io.FileAndString
 
getFileInfo(OIDHeader, String, String) - Static method in class retina.OIDHeader
 
getFileInfo(String, String, int, int) - Static method in class retina.ScriptProcessor
FileInfo raw format object for Dan's format files.
getFileInfo(String, String, int, int) - Static method in class retina.EpochSorter
Gets FileInfo raw format object for fileName, directory, width and height.
getFileInfo(String, String, int, int) - Static method in class retina.DanConverter
Gets FileInfo raw format object for fileName, directory, width and height.
getFileNames() - Method in class io.OpenPreviewDialog
End events coming from dialogwindow.
getFilenames(String) - Static method in class stereodisk.StereoDiskConventions
 
getFittedMasks() - Method in class retina.ScriptProcessor
Get the requested mask files, used to indicate which pixels on the image belong to which class.
getFloatArrayParameterLength() - Method in interface numericalMethods.function.FloatArrayParametrized
Get the length of the float array parameter.
getFloatArrayValue(float[], int) - Method in interface numericalMethods.function.FloatArrayValued
Writes the float array value into a float[].
getFloatArrayValueLength() - Method in interface numericalMethods.function.FloatArrayValued
Get the length of the float array value.
getFloatField(TextField) - Method in class VolumeJ.VJUserInterface
Get the value of a Textfield as a float.
getFloatField(TextField) - Method in class retina.OIDReconstructor
Get the value of a Textfield as a float.
getFloatField(TextField) - Method in class va.VAInterface
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.
getFloatValue() - Method in interface numericalMethods.function.FloatValued
Get the float value.
getFrameLength() - Method in class retina.OIDHeader
Get the length of each frame.
getFrames(int, String[], String) - Method in class retina.ScriptProcessor
Get a frame array from an array of filenames names, each name pointing to an ImagePlus containing the same number of frames and conditions.
getFrames(int, String, String, ImagePlus) - Method in class retina.ScriptProcessor
Make a frame array out of the ImagePlus name.
getFullTitle() - Method in class retina.OIDProcessor
 
getFullTitle(String) - Method in class retina.OIDProcessor
 
getFunction() - Method in class net.sourceforge.jannealer.AnnealingScheme
 
getGradient() - Method in class VolumeJ.VJPlane
Return the gradient of a plane (the normal vector) as a VJGradient.
getGreen() - Method in class VolumeJ.VJAlphaColor
 
getGroundTruthImagePlus(String, String, int) - Static method in class stereodisk.StereoDiskConventions
Get the image that is the observation by observer of the images basename.
getGroundTruthObserverIndex(String) - Static method in class stereodisk.StereoDiskConventions
Get the index of the observer that observed file name.
getH() - Method in class Jama.QRDecomposition
Return the Householder vectors
getH() - Method in class numericalMethods.calculus.minimizing.NumericalGradient
Get the value of h.
getHeader() - Method in class retina.OIDHeader
 
getHeaderAsString() - Method in class retina.OIDHeader
Obtains the header text as a String.
getHeaderAsString(File) - Static method in class retina.OIDHeader
Reads the header text as a String from file.
getHeaderAsString(String, String) - Static method in class retina.OIDHeader
Obtains the header text as a String from a OID file.
getHeaderFileName(String) - Static method in class retina.OIDHeader
From a file name, either header or data file, get the header file name (ending in .dat).
getHeaderInfoInt(String) - Method in class retina.OIDHeader
Read an int coming directly after the String precursor.
getHeaderInfoString(String) - Method in class retina.OIDHeader
Read a String coming directly after the String precursor.
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 retina.OIDHeader
 
getHeight() - Method in class retina.ScriptProcessor
 
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.
getImagEigenvalues() - Method in class Jama.EigenvalueDecomposition
Return the imaginary parts of the eigenvalues
getImagePlus(String, String) - Static method in class stereodisk.StereoDiskConventions
Get the image in directory with name name that is an image.
getImageProcessor() - Method in class registration.HoughTransform
Make an ImageJ ImageProcessor from this transform.
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
 
getIndices() - Method in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
getIndices() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
getInfo() - Method in class retina.OIDHeader
 
getInitialStepSize() - Method in class numericalMethods.calculus.integration.ExtrapIntegrator
 
getInitialStepSize() - Method in class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
getInitialStepSize() - Method in class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
getInputStream() - Method in class retina.OIDHeader
Get an input stream from the .kes file.
getIntegerArrayParameterLength() - Method in interface numericalMethods.function.IntegerArrayParametrized
Get the length of the integer array parameter.
getIntegerArrayValue(int[], int) - Method in interface numericalMethods.function.IntegerArrayValued
Writes the integer array value into an int[].
getIntegerArrayValueLength() - Method in interface numericalMethods.function.IntegerArrayValued
Get the length of the integer array value.
getIntegerValue() - Method in interface numericalMethods.function.IntegerValued
Get the integer value.
getIntegral(double[], int) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
getIntegral(double[], int) - Method in interface numericalMethods.calculus.integration.DoubleArrayValuedIntegrator
 
getInterpolator() - Method in class VolumeJ.VJRenderer
 
getIntField(TextField) - Method in class VolumeJ.VJUserInterface
Get the value of a Textfield as an int.
getIntField(TextField) - Method in class bd.BDUserInterface
 
getIntField(TextField) - Method in class retina.PCAWindow
 
getIntField(TextField) - Method in class retina.OIDReconstructor
Get the value of a Textfield as an int.
getIntValue() - Method in class VolumeJ.VJValue
 
getIter() - Method in class net.sourceforge.jannealer.Schedule
Gets the Iter attribute of the Schedule object
getIter() - Static method in class numericalMethods.calculus.minimizing.nmPowell
Get the value of iter.
getIter() - Static method in class numericalMethods.calculus.minimizing.ConjugateGradient
Get the value of iter.
getITMAX() - Static method in class numericalMethods.calculus.minimizing.nmBrent
Get the value of ITMAX.
getITMAX() - Static method in class numericalMethods.calculus.minimizing.DBrent
Get the value of ITMAX.
getITMAX() - Static method in class numericalMethods.calculus.minimizing.nmPowell
Get the value of ITMAX.
getITMAX() - Static method in class numericalMethods.calculus.minimizing.ConjugateGradient
Get the value of ITMAX.
getJointHistogram() - Method in class bijnum.BIJmi
 
getKeyword(int) - Method in class retina.ScriptProcessor
 
getL() - Method in class Jama.LUDecomposition
Return lower triangular factor
getL() - Method in class Jama.CholeskyDecomposition
Return triangular factor.
getLargestCircle(float[], int, int) - Method in class registration.HoughTransform
Find the largest circle in the image that has a 'good' fit.
getLeftProcessor(ImageProcessor) - Static method in class stereodisk.StereoDiskConventions
Get the left half of an image that contains a stereo pair.
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(int, int) - Method in class registration.LocatedCircle
Make a mask that masks this circle.
getMask(LocatedCircle, float[], int) - Static method in class registration.LocatedCircle
Create a mask for the field of view c
getMask(Roi, int, int) - Static method in class bijnum.BIJutil
Make a mask within an image widthxheight for Roi.
getMaskName() - Method in class retina.ScriptProcessor
 
getMatrix() - Method in class bijfit.DesignMatrix
 
getMatrix(int[], int[]) - Method in class Jama.Matrix
Get a submatrix.
getMatrix(int[], int, int) - Method in class Jama.Matrix
Get a submatrix.
getMatrix(int, int, int[]) - Method in class Jama.Matrix
Get a submatrix.
getMatrix(int, int, int, int) - Method in class Jama.Matrix
Get a submatrix.
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(double[]) - Static method in class numericalMethods.util.Arrays
Returns the maximum of target.
getMax(double[], int, double[]) - Static method in class numericalMethods.util.TupleSequences
Returns the maximum in each component of the target.
getMax(double[], int, int) - Static method in class numericalMethods.util.Arrays
Returns the maximum of target from postion to postion+length-1.
getMax(float[]) - Static method in class numericalMethods.util.Arrays
Returns the maximum of target.
getMax(float[][], int) - Static method in class VolumeJ.VJMatrix
Find the homogenuous coordinate with the highest value in an array of coordinates.
getMax(float[], int, int) - Static method in class numericalMethods.util.Arrays
Returns the maximum of target from postion to postion+length-1.
getMax(int) - Method in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
getMax(int[]) - Static method in class numericalMethods.util.Arrays
Returns the maximum of target.
getMax(int[], int, int) - Static method in class numericalMethods.util.Arrays
Returns the maximum of target from postion to postion+length-1.
getMaximalNumberOfTriangles() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
getMaxIterations() - Method in class net.sourceforge.jannealer.AnnealingScheme
 
getMaxTableSize() - Method in class numericalMethods.calculus.odeSolving.Extrap
returns maximal number of columns in interpolation table.
getMin(double[]) - Static method in class numericalMethods.util.Arrays
Returns the minimum of target.
getMin(double[], int, double[]) - Static method in class numericalMethods.util.TupleSequences
Returns the minimum in each component of the target.
getMin(double[], int, int) - Static method in class numericalMethods.util.Arrays
Returns the minimum of target from postion to postion+length-1.
getMin(float[]) - Static method in class numericalMethods.util.Arrays
Returns the minimum of target.
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.
getMin(float[], int, int) - Static method in class numericalMethods.util.Arrays
Returns the minimum of target from postion to postion+length-1.
getMin(int) - Method in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
getMin(int[]) - Static method in class numericalMethods.util.Arrays
Returns the minimum of target/.
getMin(int[], int, int) - Static method in class numericalMethods.util.Arrays
Returns the minimum of target from postion to postion+length-1.
getMinAngle(double[]) - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
getMinSimplex() - Method in class net.sourceforge.jannealer.SimplexList
Gets the Index the Simplex with the minimum value field in the SimplexList
getN() - Method in class numericalMethods.calculus.minimizing.nmLineND
Get the value of n.
getNames() - Static method in class VolumeJ.VJClassifiers
Return an array with the names of all VJClassifier classes.
getNdim() - Method in interface net.sourceforge.jannealer.ObjectiveFunction
Returns the number of dimensions for the objective function implemented
getNdim() - Method in class net.sourceforge.jannealer.test.InverseObjectiveFunction
 
getNearestKey(double) - Method in class numericalMethods.function.util.AbstractValueCacher
 
getNearestValue(double, double[], int) - Method in class numericalMethods.function.util.AbstractValueCacher
 
getNeighbor(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
getNeighborPtr(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
getNeighbors() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
getNewKey() - Method in class numericalMethods.function.util.AbstractValueCacher
 
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.
getNp() - Method in class net.sourceforge.jannealer.Schedule
Gets the Np attribute of the Schedule object
getNumber() - Method in class knn.FilterBank
Return the number of filters in this filter bank.
getNumber() - Method in class knn.StereoFilterBank
 
getNumberOfObservers(String) - Static method in class stereodisk.StereoDiskConventions
Get the number of observers that made ground truth files in directory.
getNumFaces() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
getNumOfEquations() - Method in class numericalMethods.calculus.odeSolving.RungeKutta
 
getNumOfEquations() - Method in interface numericalMethods.calculus.odeSolving.OdeSolver
 
getNumOfEquations() - Method in class numericalMethods.calculus.odeSolving.Extrap
 
getNumOfEquations() - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
getNumOfEquations() - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
getNumPoints() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
getObservationnames(String) - Static method in class stereodisk.StereoDiskConventions
Return a list of all observation stack files in directory.
getOdeSolver() - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
getOversamplingRatio() - Method in class VolumeJ.VJMatrix
Return the oversampling ratio for this (usually inverse) transformation matrix.
getP() - Method in class net.sourceforge.jannealer.Schedule
Gets the P attribute of the Schedule object
getP(int, int) - Method in class net.sourceforge.jannealer.Schedule
Gets the P attribute of the Schedule object at requested index
getPb() - Method in class net.sourceforge.jannealer.Schedule
Gets the Pb attribute of the Schedule object
getPb(int) - Method in class net.sourceforge.jannealer.Schedule
Gets the Pb attribute of the Schedule object
getPivot() - Method in class Jama.LUDecomposition
Return pivot permutation vector
getPixels() - Method in class VolumeJ.VJRenderer
Get the viewport pixel buffer.
getPlotProcessor(float[], float[], float[], float[], double, float[], String, String) - Method in class retina.ScriptProcessor
Make a graphic plot processor out of a signal with standard error of the mean sem.
getPlotProcessor(float[], float[], float[], float, float[], String) - Static method in class retina.OIDroiTCAnalyzer
Make a graphic plot processor out of a signal with standard error of the mean sem.
getPoint() - Method in class numericalMethods.calculus.minimizing.nmLineND
Get the value of point.
getPoint(int, double[]) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
getPoints() - Method in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
getPoints() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
getPoints(double[], int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
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
 
getProperties() - Method in class retina.OIDHeader
 
getQ() - Method in class Jama.QRDecomposition
Generate and return the (economy-sized) orthogonal factor
getR() - Method in class Jama.QRDecomposition
Return the upper triangular factor
getRadius() - Method in class registration.LocatedCircle
 
getRandomPermutedBlock() - Method in class retina.ScriptProcessor
Make a randomized permuted block vector that is used to decide which condition to show.
getRealEigenvalues() - Method in class Jama.EigenvalueDecomposition
Return the real parts of the eigenvalues
getRed() - Method in class VolumeJ.VJAlphaColor
 
getRegistrationParameters(float[], int) - Static method in class retina.RetinalImage
Read the stimulus flag from the bottom left pixels of the image
getRelTol() - Method in class numericalMethods.calculus.integration.ExtrapIntegrator
 
getRelTol() - Method in class numericalMethods.calculus.odeSolving.Extrap
 
getRightProcessor(ImageProcessor) - Static method in class stereodisk.StereoDiskConventions
Get the left half of an image that contains a stereo pair.
getRoi(int, int) - Method in class registration.LocatedCircle
Get an ImageJ OvalRoi corresponding to this circle.
getRow(double[][], double[], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Stores the row of matrix A in vector v.
getRow(int[][], int[], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Stores the row of matrix A in vector v.
getRowDimension() - Method in class Jama.Matrix
Get row dimension.
getRowPackedCopy() - Method in class Jama.Matrix
Make a one-dimensional row packed copy of the internal array.
getS() - Method in class Jama.SingularValueDecomposition
Return the diagonal matrix of singular values
getSaturation() - Method in class VolumeJ.VJValueHSB
 
getScale() - Method in class bijnum.BIJmi
Get the current scale.
getScriptFilename() - Method in class retina.ScriptProcessor
 
getSecondaryClassifier() - Method in class VolumeJ.VJClassifier
 
getSegments() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
getSegments() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
getSequenceNumber() - Method in class retina.OIDHeader
Get the sequence number of the .dat (and .kes file corresponding to fileName.) Assumes the filename is built as follows:
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
 
getSignalWave(int, int, int, int, int, int) - Static method in class retina.OIDAnalysis
Calculate the ideal waveform of the signal, which is -1 if the stimulus for condition j is off and +1 if it is on.
getSignificanceLevel(double) - Static method in class bijnum.BIJstats
 
getSignificanceString(double) - Static method in class bijnum.BIJstats
 
getSingularValues() - Method in class Jama.SingularValueDecomposition
Return the one-dimensional array of singular values
getSliceOrder(double, double) - Method in class VolumeJ.VJMatrix
Return the slice order as defined in Lacroutes thesis.
getSolution() - Method in class net.sourceforge.jannealer.AnnealingScheme
 
getSpecular() - Method in class VolumeJ.VJLight
 
getStackSize() - Method in class retina.OIDHeader
 
getStandardBasis(int) - Static method in class numericalMethods.calculus.minimizing.nmPowell
 
getStepperColumn() - Method in class VolumeJ.VJMatrix
Return the third column of the 3D transform matrix as a vector.
getStepSize() - Method in class numericalMethods.calculus.odeSolving.RungeKutta
 
getStepSize() - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
getStepSize() - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
getStimulus() - Method in class retina.OIDHeader
 
getStimulusData() - Method in class retina.OIDHeader
Parse the subject's name and date from the headerInfo String.
getStimulusEndFrame() - Method in class retina.OIDHeader
 
getStimulusStartFrame() - Method in class retina.OIDHeader
 
getStimulusVector(int, int, float, float) - Method in class retina.ScriptProcessor
Make a square wave 'stimulus vector' i.e.
getString() - Method in class io.FileAndString
 
getString(int) - Method in class retina.ScriptProcessor
 
getSubject() - Method in class retina.OIDHeader
 
getSupport(float, int) - Static method in class FlowJ.FlowJLucas
Return the number of frames needed for specific sigmat and gradient type.
getT() - Method in class numericalMethods.calculus.minimizing.nmLineND
Get the value of t.
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.
getTuple(double[], int, int, double[]) - Static method in class numericalMethods.util.TupleSequences
Returns a tupble of the target.
getType(Object[]) - Method in class VolumeJ.VJProjection
Return the datatype of the array components.
getU() - Method in class Jama.SingularValueDecomposition
Return the left singular vectors
getU() - Method in class Jama.LUDecomposition
Return upper triangular factor
getUseDBrent() - Static method in class numericalMethods.calculus.minimizing.ConjugateGradient
Get the value of useDBrent.
getV() - Method in class Jama.SingularValueDecomposition
Return the right singular vectors
getV() - Method in class Jama.EigenvalueDecomposition
Return the eigenvector matrix
getValue() - Method in class VolumeJ.VJAlphaColor
 
getValue() - Method in class net.sourceforge.jannealer.Simplex
Gets the Value attribute of the Simplex object
getValue(double[]) - Method in class numericalMethods.calculus.minimizing.NumericalGradient
 
getValue(double[]) - Method in class numericalMethods.calculus.minimizing.nmLineND
 
getValue(double[]) - Method in class numericalMethods.calculus.minimizing.Quadric
 
getValue(double[]) - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.RealSinus
 
getValue(double[]) - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.ComplexSinus
 
getValue(double[]) - Method in class numericalMethods.function.util.DoubleArrayValueCacher
 
getValue(int, int) - Method in class of3d.OF3DSpot
 
getValues() - Method in class registration.HoughTransform
Get the Hough transform value vector.
getVector(VJVoxelLoc) - Method in class of3d.OF3DDeformation
 
getVertex() - Method in class net.sourceforge.jannealer.Simplex
Gets the Vertex attribute of the Simplex object
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
 
getvote(float[], int) - Static method in class knn.ANN
 
getWaveform() - Method in class retina.ScriptProcessor
 
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 retina.OIDHeader
 
getWidth() - Method in class retina.ScriptProcessor
 
getWidth() - Method in class volume.Volume
 
getWindowNames(int[]) - Method in class VolumeJ.VJUserInterface
Get the names (by getTitle() method) from a list of windows.
getWindowNames(int[]) - Method in class bd.BDUserInterface
 
getWindows() - Method in class bd.BDUserInterface
 
getx() - Method in class VolumeJ.VJGradient
 
getx() - Method in class VolumeJ.VJLight
 
getx() - Method in class VolumeJ.VJVoxelLoc
Get the x-position.
getX() - Method in class registration.LocatedCircle
 
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() - Method in class net.sourceforge.jannealer.Schedule
Gets the Y attribute of the Schedule object
getY() - Method in class registration.LocatedCircle
 
gety(int) - Method in class VolumeJ.VJGradient
 
getY(int) - Method in class net.sourceforge.jannealer.Schedule
Gets the Y attribute of the Schedule object
getY(int, int) - Method in class FlowJ.FlowJFlow
 
getYb() - Method in class net.sourceforge.jannealer.Schedule
Gets the Yb attribute of the Schedule object
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
 
GLIMIT - Static variable in class numericalMethods.calculus.minimizing.nmBracket
 
GOLD - Static variable in class numericalMethods.calculus.minimizing.nmBracket
 
Golden - class numericalMethods.calculus.minimizing.Golden.
 
Golden() - Constructor for class numericalMethods.calculus.minimizing.Golden
 
gp - Static variable in class FlowJ.FlowJSpotNoise
 
grabFrame(short[][], int) - Method in class va.TimedAcquisition
Grab the current frame and copy into the framebuffer.
gradAtT - Variable in class numericalMethods.calculus.minimizing.LineNDDBrent.projectedGradient
 
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
 
gui - Variable in class va.VideoWatch
 
gui - Variable in class va.VideoAcq
 

H

h - Variable in class numericalMethods.calculus.minimizing.NumericalGradient
 
halfwidth - Variable in class volume.Kernel
 
hasExteriorPoints - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
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
 
HBARHEIGHT - Static variable in class retina.ScriptProcessor
 
HBARWIDTH - Static variable in class retina.ScriptProcessor
 
header - Variable in class retina.OIDProcessor
 
HEADER_EXTENSION - Static variable in class retina.OIDHeader
 
headerInfo - Variable in class retina.OIDHeader
 
headerSize - Static variable in class retina.OIDHeader
 
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 registration.HoughTransform
 
height - Static variable in class retina.DanConverter
 
height - Static variable in class stereodisk.StereoDiskAnalyzer
 
height - Variable in class va.VAInterface
 
height - Variable in class va.TimedAcquisition
 
height - Variable in class va.ThreadCompression
 
height - Variable in class volume.Volume
Dimensions of the volume.
HEIGHT - Static variable in class retina.OIDHeader
 
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_scales - Static variable in class knn.FeatureComputer
 
Hessian() - Constructor for class volume.Hessian
 
HESSIANSCALE - Static variable in class retina.RetinalImage
Optimal scale (unitless, stddev of the Gaussian) of the Hessian tensor for 256x256 retinal images.
highestOrderSum(double[]) - Static method in class numericalMethods.calculus.integration.NewtonCotes
 
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.
HN - Static variable in class retina.ScriptProcessor
 
HoughTransform - class registration.HoughTransform.
This class implements a Hough transformer.
HoughTransform(int, int, double) - Constructor for class registration.HoughTransform
New Hough transform.
HoughTransform(Rectangle, double) - Constructor for class registration.HoughTransform
New Hough transform for a ROI.
Householder - class numericalMethods.algebra.linear.decompose.Householder.
Computes for a matrix A the matrices Q and R complying A=Q·R.
Householder() - Constructor for class numericalMethods.algebra.linear.decompose.Householder
 
hsb - Variable in class VolumeJ.VJValueHSB
 
HSPACING - Static variable in class retina.ScriptProcessor
 
HSTART - Static variable in class retina.ScriptProcessor
 
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
hypot(double, double) - Static method in class Jama.util.Maths
sqrt(a^2 + b^2) without under/overflow.

I

i - Static variable in class FlowJ.FlowJSpotNoise
 
I - Variable in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
ic - Variable in class retina.PCAWindow
 
identity(int) - Static method in class numericalMethods.algebra.group.Permutation
Returns an identity permutation of the desired length.
identity(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Replaces the int[] parameter with the identity of the same length.
identity(int, int) - Static method in class Jama.Matrix
Generate identity matrix
iList - Variable in class VolumeJ.VJUserInterface
 
iList - Variable in class bd.BDUserInterface
 
image(long[][]) - Static method in class numericalMethods.geometry.latticeReduction.ExactLLL
 
image(long[][], long[][]) - Static method in class numericalMethods.geometry.latticeReduction.ExactLLL
 
image(long[][], long[][], long[]) - Static method in class numericalMethods.geometry.latticeReduction.ExactLLL
 
imageChoice - Variable in class bd.BDUserInterface
 
imageFeaturePixels(int, String, String[]) - Static method in class stereodisk.StereoDiskAnalyzer
Obtain all features names for a single image i.
imagescience.features.src - package imagescience.features.src
 
imagescience.images.src - package imagescience.images.src
 
imagescience.utilities.src - package imagescience.utilities.src
 
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.
IMAXX - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
imp - Variable in class VolumeJ.VJRenderViewInteractive
 
imp - Variable in class bd.BDUserInterface
 
imp - Variable in class va.VideoWatch
 
imp - Variable in class va.VideoAcq
 
imp - Variable in class volume.Diffusion
 
impAnalysis - Variable in class retina.ScriptProcessor
 
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
 
increaseIter(int) - Method in class net.sourceforge.jannealer.Schedule
Increments the attribute iter by dIter
index - Static variable in class FlowJ.FlowJSpotNoise
 
index - Variable in class VolumeJ.VJValue
 
index - Variable in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
index - Variable in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
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.SVDCException
 
init() - Method in class retina.ScriptProcessor
 
init(double[]) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
init(double, double, double, double, int, int) - Static method in class numericalMethods.geometry.meshGeneration.ruppert.Initializer
 
init(double, double, double, double, int, int, double[], int[]) - Static method in class numericalMethods.geometry.meshGeneration.ruppert.Initializer
 
init(Ruppert) - Method in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer
 
init(ScriptProcessor) - Method in class retina.OIDAnalyzer
 
init(ScriptProcessor) - Method in class retina.OIDTimecourseAnalyzer
 
init(ScriptProcessor) - Method in class retina.OIDMapsFitter
 
init(ScriptProcessor) - Method in class retina.OIDroiAnalyzer
 
init(ScriptProcessor) - Method in class retina.OIDPCAAnalyzer
 
init(ScriptProcessor) - Method in class retina.OIDROItimecourseAnalyzer
 
init(ScriptProcessor) - Method in interface retina.OIDBaseAnalyzer
 
init(String) - Method in class retina.OIDroiAnalyzer
 
init(String) - Method in class retina.OIDROItimecourseAnalyzer
Hook for initialization: the first of a sequence that is analyzed.
initClassifiers() - Static method in class VolumeJ.VJClassifiers
 
initClassifiers() - Static method in class of3d.OF3DClassifiers
 
initializeP() - Method in class net.sourceforge.jannealer.Schedule
Description of the Method
Initializer - class numericalMethods.geometry.meshGeneration.ruppert.Initializer.
 
Initializer() - Constructor for class numericalMethods.geometry.meshGeneration.ruppert.Initializer
 
initializing - Variable in class VolumeJ.VJUserInterface
 
initialN - Variable in class va.TimedAcquisition
 
initialStepSize - Variable in class numericalMethods.calculus.integration.ExtrapIntegrator
 
initialStepSize - Variable in class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
initialStepSize - Variable in class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
INITIALSTRING - Static variable in class va.TimedAcquisition
 
initiated - Variable in class retina.OIDWindow
 
initVideo() - Method in class va.VAInterface
 
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.
instance - Static variable in class va.VAInterface
 
IntegerArrayParametrized - interface numericalMethods.function.IntegerArrayParametrized.
Interface for objects that represent functions of an integer array parameter.
IntegerArrayValued - interface numericalMethods.function.IntegerArrayValued.
Interface for objects that represent integer array valued functions.
IntegerParametrized - interface numericalMethods.function.IntegerParametrized.
Interface for objects that represent functions of an integer parameter.
IntegerValued - interface numericalMethods.function.IntegerValued.
Interface for objects that represent integer valued functions.
integrate(double[], double[]) - Static method in class numericalMethods.calculus.functionApproximation.ChebyshevApproximation
Simply calls integate(c, cInt, factor) with double factor = 1.0.
integrate(double[], double[], double) - Static method in class numericalMethods.calculus.functionApproximation.ChebyshevApproximation
Given the coefficients c[j] of a Chebyshev series approximating some function f(x), calculates the coefficients cInt[j] of a Chebyshev series approximating factor × ∫ f(x)dx.
integrate(DoubleParametrized, DoubleArrayValued, double, double, double[]) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
integrate(DoubleParametrized, DoubleArrayValued, double, double, double[]) - Method in interface numericalMethods.calculus.integration.DoubleArrayValuedIntegrator
 
integrate(DoubleParametrized, DoubleArrayValued, double, double, double[], int) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
integrate(DoubleParametrized, DoubleArrayValued, double, double, double[], int) - Method in interface numericalMethods.calculus.integration.DoubleArrayValuedIntegrator
 
integrateTo(double) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
integrateTo(double) - Method in class numericalMethods.calculus.integration.ExtrapIntegrator
 
integrateTo(double) - Method in interface numericalMethods.calculus.integration.DoubleArrayValuedIntegrator
 
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 Jama.Matrix
Matrix inverse or pseudoinverse
inverse() - Method in class VolumeJ.VJMatrix
Invert this matrix.
inverse(float[][]) - Static method in class bijnum.BIJmatrix
Invert a symmetric matrix m.
inverse(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the inverse permutation.
inverse(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Changes result to the inverse permutation of s.
InverseObjectiveFunction - class net.sourceforge.jannealer.test.InverseObjectiveFunction.
Normally this would just be an anonymous class, but we're using it from two classes.
InverseObjectiveFunction() - Constructor for class net.sourceforge.jannealer.test.InverseObjectiveFunction
 
InverseTest - class net.sourceforge.jannealer.test.InverseTest.
Use simulated annealing to calculate the inverse of two functions with three variables a=sin(x)*exp(y)*z b=exp(x)*sin(y)
InverseTest() - Constructor for class net.sourceforge.jannealer.test.InverseTest
 
Inversion - class numericalMethods.algebra.linear.Inversion.
Computes the inverse of a square matrix.
Inversion() - Constructor for class numericalMethods.algebra.linear.Inversion
 
inversions(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Gives the inversion vector, that is, for each index, the number of greater indices to its left in the permutation.
inversions(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Gives the inversion vector, that is, for each index, the number of greater indices to its left in the permutation.
inversionsFun(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Gives the inversion vector of a permutation in functional notation, that is, for each index, the number of greater indices to its left in the permutation.
inversionsFun(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Gives the inversion vector of a permutation in functional notation, that is, for each index, the number of greater indices to its left in the permutation.
invert - Variable in class retina.OIDWindow
Number of standarddeviations from average eye-motion to qualify as abnormal or blink.
invertMask(float[]) - Static method in class retina.OIDroiAnalyzer
 
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
 
ip - Variable in class retina.PCAWindow
 
ip - Variable in class va.VideoWatch
 
ip - Variable in class va.VideoAcq
 
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.
isDebug() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
isDerangement(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns whether the given int[] is a valid derangement (permutation without fixed point) of the indices 0..length-1.
isDerangement(int[], boolean[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns whether the given int[] is a valid derangement (permutation without fixed point) of the indices 0..length-1.
isDerangement(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns whether the given int[] is a valid derangement (permutation without fixed point) of the indices 0..length-1.
isFullRank() - Method in class Jama.QRDecomposition
Is the matrix full rank?
isGrayscale() - Method in class VolumeJ.VJAlphaColor
 
isGroundTruthBackground(Color) - Static method in class stereodisk.StereoDiskConventions
 
isGroundTruthCup(Color) - Static method in class stereodisk.StereoDiskConventions
Cups are somewhat *&%$&^ yellowish, i.e., G >= 253 and B < = 5.
isGroundTruthDisk(Color) - Static method in class stereodisk.StereoDiskConventions
Disks are somewhat *&%$&^ red, i.e..
isIndexed() - Method in class volume.VolumeRGB
 
isNonsingular() - Method in class Jama.LUDecomposition
Is the matrix nonsingular?
isOIDDATFile(String) - Static method in class retina.OIDHeader
Check whether the name can be an OID .dat file, the file with the textual header info.
isOIDFile(String) - Static method in class retina.OIDHeader
Check whether the name can be an OID file.
ISOSURFACE - Static variable in class VolumeJ.VJUserInterface
 
ISOSURFACE - Static variable in class VolumeJ.VJClassifiers
 
isPermutation(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns whether the given int[] is a valid permutation of the indices 0..length-1.
isPermutation(int[], boolean[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns whether the given int[] is a valid permutation of the indices 0..length-1.
isPermutation(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns whether the given int[] is a valid permutation of the indices 0..length-1.
isRightEye() - Method in class retina.OIDHeader
 
isSPD() - Method in class Jama.CholeskyDecomposition
Is the matrix symmetric and positive definite?
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 bd.BDUserInterface
 
itemStateChanged(ItemEvent) - Method in class io.OpenPreviewDialog
 
itemStateChanged(ItemEvent) - Method in class va.VAInterface
React to action e.
iter - Static variable in class numericalMethods.calculus.minimizing.nmPowell
 
iter - Static variable in class numericalMethods.calculus.minimizing.ConjugateGradient
 
iterations - Static variable in class volume.Diffusion
 
iterations - Static variable in class volume.Diffusion3D
 
ITMAX - Static variable in class numericalMethods.calculus.minimizing.nmBrent
 
ITMAX - Static variable in class numericalMethods.calculus.minimizing.DBrent
 
ITMAX - Static variable in class numericalMethods.calculus.minimizing.nmPowell
 
ITMAX - Static variable in class numericalMethods.calculus.minimizing.ConjugateGradient
 
IwasawaFactorization - class numericalMethods.algebra.loopGroup.IwasawaFactorization.
Computes the Iwasawa factorization of a GL_n(C)-valued loop.
IwasawaFactorization() - Constructor for class numericalMethods.algebra.loopGroup.IwasawaFactorization
 
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
 
j - Static variable in class va.VideoWatch
 
j - Static variable in class va.VideoAcq
 
Jacobi - class bijnum.Jacobi.
Deprecated.  
Jacobi(int) - Constructor for class bijnum.Jacobi
Deprecated. Create the eigenvectors and eigenvalues that will be computed.
Jama - package Jama
 
Jama.test - package Jama.test
 
Jama.util - package Jama.util
 
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 - Static variable in class stereodisk.StereoDiskANNTester
 
k - Static variable in class stereodisk.StereoDiskROC
 
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
 
kappa(float[]) - Static method in class bijnum.BIJstats
Compute kappa for a 2x2 table.
kDistances - Variable in class bijnum.BIJknn
Some variables that I do not want to allocate for every element.
keplerSum(double[]) - Static method in class numericalMethods.calculus.integration.NewtonCotes
 
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
 
keyPressed(KeyEvent) - Method in class va.VAInterface
 
keyReleased(KeyEvent) - Method in class VolumeJ.VJUserInterface
 
keyReleased(KeyEvent) - Method in class va.VAInterface
 
keyTyped(KeyEvent) - Method in class VolumeJ.VJUserInterface
React to action e.
keyTyped(KeyEvent) - Method in class va.VAInterface
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.
kill() - Method in class va.VideoWatch
The kill method is called when the watcher is to stop.
kill() - Method in class va.TimedAcquisition
The kill method is called when the watcher is to stop.
kill() - Method in class va.VideoAcq
The kill method is called when the watcher is to stop.
kinc - Variable in class VolumeJ.VJCell
 
kIndices - Variable in class bijnum.BIJknn
 
kmax - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer
 
KMAXX - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
knn - package knn
 
koffset - Variable in class VolumeJ.VJReconstructor
 
koffset - Variable in class VolumeJ.VJRenderer
Start of rays in viewspace.
koffset - Variable in class of3d.OF3DDeformer
 
kopt - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer
 

L

l - Variable in class bd.BDSeparatorLattice
 
L(float[], int, int, double, double, String) - Static method in class knn.FilterBank
Compute an L filter of order, scale and orientation.
L(float[], int, int, double, float[]) - Static method in class knn.FilterBank
Compute a number of convolutions L of image (column vector) and width width, with a Gaussian order-th kernel at scale s and orientations theta.
labelConf - Variable in class retina.PCAWindow
 
labelFrameRate - Variable in class va.VAInterface
 
labelRMSE - Variable in class retina.PCAWindow
 
labelStatus - Variable in class va.VAInterface
 
labelStatus1 - Variable in class va.VAInterface
 
labelVar - Variable in class retina.PCAWindow
 
laguerAllRoots(double[], double[], int, double, double[], double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
laguerOneRoot(double[], double[], int, double, double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
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.
largestDiameter(float[], int, double) - Static method in class retina.RetinalImage
Get the diameter of a circle defined as edge pixels.
largestDoubleArea() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
largestEdge(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
lastFrame(ImageStack, float, int) - Static method in class FlowJ.FlowJLucas
Return the last frame for which you can compute the flow.
lastInCach - Variable in class numericalMethods.function.util.AbstractValueCacher
 
lastKey - Variable in class numericalMethods.function.util.AbstractValueCacher
 
lcm(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Computes the least common multiple of several numbers.
lcm(int, int) - Static method in class numericalMethods.algebra.group.Permutation
Computes the least common multiple of two numbers.
LEAST_DISTANCE_FACTOR - Static variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
leastEdgeSqr() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
legalizeEdge(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
legalizeNewFaces() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
legalizeNewFaces() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
length - Variable in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
length - Static variable in class retina.OIDReconstructor
 
length - Variable in class retina.OIDProcessor
Other parameters describing the layout of aggregate.
length - Variable in class volume.HyperVolume
 
LENGTH - Static variable in class retina.ScriptProcessor
The number of frames for each condions.
length() - Method in class knn.Feature
 
length() - Method in class knn.Features
 
length(int, int) - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
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
 
linComb(double, double, double[], double[], int, double, double, double[], double[], int, double[], double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
line(float[], int, int, int) - Static method in class registration.HoughTransform
Hough transform image for lines with angle theta and distance from center.
LINEAR - Static variable in class VolumeJ.VJClassifiers
 
linear(float[], float[]) - Static method in class bijnum.BIJfit
Given a line with points x, y, fit a line y = a1 + a2x through them with linear least squares regression.
linearCorr - Variable in class retina.OIDWindow
 
linearcorrect(double[]) - Static method in class bijnum.BIJstats
Corrects data for a linear trend.
linearCorrect(float[][], float[]) - Static method in class retina.OIDProcessor
Do linear correction on the ROI of all images in the sequence.
LineNDDBrent - class numericalMethods.calculus.minimizing.LineNDDBrent.
 
LineNDDBrent.projectedGradient - class numericalMethods.calculus.minimizing.LineNDDBrent.projectedGradient.
 
LineNDDBrent.projectedGradient(LineNDDBrent) - Constructor for class numericalMethods.calculus.minimizing.LineNDDBrent.projectedGradient
 
LineNDDBrent(DoubleArrayParametrized, DoubleValued, DoubleArrayValued) - Constructor for class numericalMethods.calculus.minimizing.LineNDDBrent
 
LineNDDBrent(DoubleArrayParametrized, DoubleValued, DoubleArrayValued, double[], double[]) - Constructor for class numericalMethods.calculus.minimizing.LineNDDBrent
 
linzeros(float[][], float[], int, int) - Static method in class knn.StereoFilterBank
Fit a linear regression line to each of the vectors 0..N*width in matrix[Nxwidth][M] (which is an image of vectors) and return a vector with the zerocrossings of the regression line.
linzerosOld(float[][], float[], int, int) - Static method in class knn.StereoFilterBank
Fit a linear regression line to each of the vectors 0..N*width in matrix[Nxwidth][M] (which is an image of vectors) and return a vector with the zerocrossings of the regression line.
list - Variable in class io.OpenPreviewDialog
 
list - Static variable in class stereodisk.StereoDiskFeatureConverter
 
LLL - class numericalMethods.geometry.latticeReduction.LLL.
 
LLL() - Constructor for class numericalMethods.geometry.latticeReduction.LLL
 
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(int, int, int, String, String) - Static method in class retina.OIDtc
Load a [][] matrix from a file.
load(Object[], int) - Method in class volume.VolumeRGB
Fill the brightness volume b with the int[] slices, starting at slice start.
loadFeatures(String, String[], int[][], boolean) - Static method in class stereodisk.StereoDiskAnalyzer
 
loadFloatImage(String, String, int) - Static method in class stereodisk.StereoDiskAnalyzer
Load the i'th image in name as a float[][].
loadFloatImages(String, String) - Static method in class stereodisk.StereoDiskAnalyzer
Load the images in name (a mutli-image TIFF file) as a float[][].
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
 
loadProjectedStimulusMaps(String, String) - Method in class retina.ScriptProcessor
Read projected stimulus maps and return as a FloatProcessor array.
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.
loadStimulusMaps(String, String) - Method in class retina.ScriptProcessor
Create stimulus maps file and return as a ByteProcessor array.
LocatedCircle - class registration.LocatedCircle.
This is a circle located in an image and is used by circle finding algorithms.
LocatedCircle(double, double, double) - Constructor for class registration.LocatedCircle
Create new HoughCircle.
LocatedCircle(double, double, double, double) - Constructor for class registration.LocatedCircle
Create new HoughCircle.
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
 
lookupKeyword(String) - Method in class retina.ScriptProcessor
Lookup the corresponding index for a keyword.
lostOwnership(Clipboard, Transferable) - Method in class FlowJ.FlowJUserInterface
 
lostOwnership(Clipboard, Transferable) - Method in class VolumeJ.VJUserInterface
 
lostOwnership(Clipboard, Transferable) - Method in class bd.BDUserInterface
 
LR - class numericalMethods.algebra.linear.decompose.LR.
Computes for a square matrix A the matrices L and R complying A=L·R.
LR() - Constructor for class numericalMethods.algebra.linear.decompose.LR
 
lu() - Method in class Jama.Matrix
LU Decomposition
LUDecomposition - class Jama.LUDecomposition.
LU Decomposition.
LUDecomposition(Matrix) - Constructor for class Jama.LUDecomposition
LU Decomposition
lut - Variable in class VolumeJ.VJClassifierLevoy
 
lutChoice - Variable in class VolumeJ.VJUserInterface
 
LXB - class numericalMethods.algebra.linear.solve.LXB.
Computes for a system of equations L·X=B with given left triangular matrix L and matrix B the solving matrix X.
LXB() - Constructor for class numericalMethods.algebra.linear.solve.LXB
 

M

m - Variable in class VolumeJ.VJRenderView
State variables.
m - Variable in class VolumeJ.VJRenderer
Transformation matrix and inverse.
mag - Static variable in class bijfit.Maximum
The magnitude of the peak as found by findSubpixel
mag() - Method in class bijnum.BIJfft
Compute power spectrum of FFT 1-D.
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.
main(String[]) - Static method in class Jama.test.TestMatrix
 
main(String[]) - Static method in class net.sourceforge.jannealer.test.InverseTest
 
main(String[]) - Static method in class net.sourceforge.jannealer.test.Trivial
 
main(String[]) - Static method in class net.sourceforge.jannealer.test.TestAnneal
 
main(String[]) - Static method in class net.sourceforge.jannealer.test.ConfigureAnnealing
 
main(String[]) - Static method in class numericalMethods.algebra.linear.TestInversion
 
main(String[]) - Static method in class numericalMethods.algebra.linear.TestDeterminant
 
main(String[]) - Static method in class numericalMethods.algebra.linear.decompose.TestPLR
 
main(String[]) - Static method in class numericalMethods.algebra.linear.decompose.TestTridiagonal
 
main(String[]) - Static method in class numericalMethods.algebra.linear.decompose.TestCholesky
 
main(String[]) - Static method in class numericalMethods.algebra.linear.decompose.TestQR
 
main(String[]) - Static method in class numericalMethods.algebra.linear.decompose.TestLR
 
main(String[]) - Static method in class numericalMethods.algebra.linear.decompose.TestHouseholder
 
main(String[]) - Static method in class numericalMethods.algebra.linear.solve.TestAXB
 
main(String[]) - Static method in class numericalMethods.algebra.linear.solve.TestRXB
 
main(String[]) - Static method in class numericalMethods.algebra.linear.solve.TestLXB
 
main(String[]) - Static method in class numericalMethods.calculus.functionApproximation.TestChebyshevApproximation
 
main(String[]) - Static method in class numericalMethods.calculus.integration.TestNewtonCotes
 
main(String[]) - Static method in class numericalMethods.calculus.integration.ExampleIntegration
Integrates the above given function in the interval [a,b].
main(String[]) - Static method in class numericalMethods.calculus.minimizing.ExampleND
 
main(String[]) - Static method in class numericalMethods.calculus.minimizing.Example1D
 
main(String[]) - Static method in class numericalMethods.calculus.odeSolving.ExampleODE
Solves the above given ode in the time interval [0,1] with start values x0 and y0 given in the argument list.
main(String[]) - Static method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson
 
main(String[]) - Static method in class numericalMethods.calculus.specialFunctions.TestClausen
 
main(String[]) - Static method in class numericalMethods.calculus.specialFunctions.Clausen
Prints Chebyshev coefficients to stdout, which are to be pasted into the code.
main(String[]) - Static method in class numericalMethods.calculus.specialFunctions.TestGamma
 
main(String[]) - Static method in class numericalMethods.geometry.latticeReduction.TestLLL
 
main(String[]) - Static method in class numericalMethods.geometry.latticeReduction.TestExactLLL
 
main(String[]) - Static method in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer
 
main(String[]) - Static method in class retina.OIDAnalyzer
 
main(String[]) - Static method in class retina.OIDtc
 
main(String[]) - Static method in class retina.EpochSorter
 
main(String[]) - Static method in class retina.AngiographAnalyzer
 
main(String[]) - Static method in class retina.DanConverter
 
main(String[]) - Static method in class stereodisk.StereoDiskAnalyzer
 
main(String[]) - Static method in class stereodisk.StereoDiskFeatureConverter
 
main(String[]) - Static method in class stereodisk.StereoDiskGroundTruthConverter
 
main(String[]) - Static method in class stereodisk.StereoDiskGroundTruthAnalyzer
 
main(String[]) - Static method in class stereodisk.StereoDiskANNTester
 
main(String[]) - Static method in class stereodisk.StereoDiskROC
 
main(String[]) - Static method in class stereodisk.StereoDiskANNMaker
 
main(String[]) - Static method in class stereodisk.StereoDiskPGMToFeatureConverter
 
main(String[]) - Static method in class stereodisk.StereoDiskIxConverter
 
main(String[]) - Static method in class stereodisk.StereoDiskAutomaticAligner
 
main(String[]) - Static method in class stereodisk.StereoCupRimClassifier
 
main(String[]) - Static method in class stereodisk.StereoDiskPGMConverter
 
main(String[]) - Static method in class stereodisk.StereoDiskSlideCropper
 
makeBarMasks(String, int, int, float, float, float, float, float, float, boolean) - Static method in class retina.OIDroiAnalyzer
 
makeBitReverseTable(int) - Method in class bijnum.BIJfht
 
makeCopies() - Method in class retina.PCAWindow
 
makeDiagonalControlMask(int, int, int, int, int, int, float, String) - Static method in class retina.OIDroiAnalyzer
 
makeDiagonalMask(int, int, int, int, int, int, float, String) - Static method in class retina.OIDroiAnalyzer
 
makeDiagonalMasks(String, int, int, float, float, float, float, boolean) - Static method in class retina.OIDroiAnalyzer
 
makeFeaturesName(String) - Static method in class stereodisk.StereoDiskConventions
Make a features filename for basename.
makeGroundTruthName(String) - Static method in class stereodisk.StereoDiskConventions
Make a ground truth filename for basename.
makeHorizontalControlMask(float[], int, int, float, float, float, float, float) - Static method in class retina.OIDroiAnalyzer
Make a so-called horizontal stimulus mask (a vertical bar).
makeHorizontalHalfMask(int, int, float, float, float, float, float, int) - Static method in class retina.OIDroiAnalyzer
Make a so-called horizontal half mask, i.e.
makeHorizontalMask(int, int, float, float, float, float, float) - Static method in class retina.OIDroiAnalyzer
Make a so-called horizontal stimulus mask (a vertical bar).
makeMaskedNaN(float[], float[]) - Static method in class registration.RegisterRetina
Mask the pixels in a vector image by setting all pixels that have mask == 0 to NaN.
makeMasks(String, boolean) - Method in class retina.OIDroiAnalyzer
 
makeMasks(String, boolean) - Method in class retina.OIDroiTCAnalyzer
Make ROI masks.
makePointArray(double[][]) - Static method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
makePower2(float[]) - Static method in class bijnum.BIJutil
Mirror a vector so that is has power of 2 length and does not contain extra edges.
makeSegments(double[][]) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
makeSinCosTables() - Method in class bijnum.BIJfft
Calculate the sin and cos tables for the current vector length.
makeSinCosTables(int) - Method in class bijnum.BIJfht
 
makeStereoPairName(String) - Static method in class stereodisk.StereoDiskConventions
Make a stereopair filename for basename.
makeTControlMask(float[], int, int, float, float, float, float, float, float, float, float) - Static method in class retina.OIDroiAnalyzer
Make a T-shaped control mask with all mask pixels 1.
makeTMask(int, int, float, float, float, float, float, float, float, float) - Static method in class retina.OIDroiAnalyzer
Make a T-shaped mask with all mask pixels 1.
makeTMasks(String, int, int, float, float, float, float, float, float, boolean) - Static method in class retina.OIDroiAnalyzer
 
makeValid(String) - Method in class retina.ScriptProcessor
 
makeVerticalControlMask(float[], int, int, float, float, float, float, float) - Static method in class retina.OIDroiAnalyzer
Make a so-called vertical control mask (a horizontal bar).
makeVerticalHalfMask(int, int, float, float, float, float, float, int) - Static method in class retina.OIDroiAnalyzer
Make a so-called vertical half mask, i.e.
makeVerticalMask(int, int, float, float, float, float, float) - Static method in class retina.OIDroiAnalyzer
Make a so-called vertical stimulus mask (a horizontal bar).
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
 
mapClean() - Method in class retina.PCAWindow
Compute a cleaned image sequence from only the attractive eigenvalues.
mapCoordinates() - Method in class retina.PCAWindow
Map the eigenvector matrix into an image.
mapCorrelations(float[][][], float[][][], String, String) - Static method in class retina.OIDroiTCAnalyzer
 
mapfile - Variable in class retina.ScriptProcessor
 
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
 
mapImageCorrelations(float[], String) - Method in class retina.PCAWindow
Show the correlations and projection coordinates of an image with the PCA eigenimages.
mapIndicatorFunction() - Method in class retina.PCAWindow
Compute the indicator function image for two conditions.
mappingChoice - Variable in class VolumeJ.VJUserInterface
 
mapTruncatedDifference() - Method in class retina.PCAWindow
Compute an image that is the truncated difference of the stimulus and non-stimulus conditions stim.
mapVariance() - Method in class retina.PCAWindow
Map the variances and fractional variances for each component.
MarchingCubes - class numericalMethods.geometry.hyperSurface.MarchingCubes.
 
MarchingCubes() - Constructor for class numericalMethods.geometry.hyperSurface.MarchingCubes
 
MarchingCubes(double[][][], double, double[], double[]) - Constructor for class numericalMethods.geometry.hyperSurface.MarchingCubes
 
markSegment(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
mask - Variable in class registration.Register
The mask if needed.
mask(float[], float[]) - Static method in class bijnum.BIJmatrix
Return a vector containing only the elements in v that have a mask value != 0.
maskfile - Variable in class retina.ScriptProcessor
 
MASKFILE - Static variable in class retina.ScriptProcessor
 
MASKFREQUENCY - Static variable in class retina.ScriptProcessor
 
maskIndex - Variable in class VolumeJ.VJClassifierLevoy
 
maskIntensity - Variable in class VolumeJ.VJClassifierLevoy
 
maskMagnitude - Variable in class VolumeJ.VJClassifierLevoy
 
MASKSCALE - Static variable in class retina.ScriptProcessor
 
masksFitted - Variable in class retina.OIDMapsFitter
 
maskTimecourseAnalysis(float[][], float[][][][], float[][], float[][], int, int, int, float[][], int) - Static method in class retina.OIDAnalysis
Timecourse analysis using masks over all frames.
MASKTYPE - Static variable in class retina.ScriptProcessor
 
MASKTYPE_BARS - Static variable in class retina.ScriptProcessor
 
MASKTYPE_BLOCKS - Static variable in class retina.ScriptProcessor
 
MASKTYPE_CENTRAL - Static variable in class retina.ScriptProcessor
 
MASKTYPE_DIAG - Static variable in class retina.ScriptProcessor
 
MASKTYPE_PANELS - Static variable in class retina.ScriptProcessor
 
MASKTYPE_T - Static variable in class retina.ScriptProcessor
 
Maths - class Jama.util.Maths.
 
Maths() - Constructor for class Jama.util.Maths
 
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.
Matrix - class Jama.Matrix.
Jama = Java Matrix class.
Matrix(double[][]) - Constructor for class Jama.Matrix
Construct a matrix from a 2-D array.
Matrix(double[][], int, int) - Constructor for class Jama.Matrix
Construct a matrix quickly without checking arguments.
Matrix(double[], int) - Constructor for class Jama.Matrix
Construct a matrix from a one-dimensional packed array
Matrix(int, int) - Constructor for class Jama.Matrix
Construct an m-by-n matrix of zeros.
Matrix(int, int, double) - Constructor for class Jama.Matrix
Construct an m-by-n constant 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.
matrixFromImageStack(ImageStack) - Static method in class bijnum.BIJutil
Access the data in the ImageStack in imp into a float[][] matrix for further processing.
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.
MatrixOperations - class numericalMethods.algebra.linear.MatrixOperations.
This class handles the basic operations with matrices .
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.
max - Variable in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
MAX_NUM_OF_STEPS - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
MAX_NUM_OF_STEPS - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
MAX_NUM_OF_STEPS - Static variable in class numericalMethods.calculus.rootFinding.NewtonRaphson
Default maximum number of steps performed in Newton´s method: 50.
maxAbs(double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Locates the entry with the greatest absolute value.
maxAbs(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Locates the entry with the greatest absolute value.
maximalNumberOfTriangles - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
Maximum - class bijfit.Maximum.
This class implements methods to find the maximum pixel value and the location of the maximum value in vectors and 2D images.
Maximum() - Constructor for class bijfit.Maximum
 
maxIntensity - Variable in class VolumeJ.VJClassifierLevoy
 
maxN - Variable in class bijnum.BIJfht
 
maxNob - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
maxNof - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
maxNop - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
maxp - Variable in class FlowJ.FlowJMapper
 
maxp - Variable in class FlowJ.FlowJSpotNoise
 
maxq - Variable in class FlowJ.FlowJMapper
 
maxq - Variable in class FlowJ.FlowJSpotNoise
 
maxvalue - Variable in class registration.HoughTransform
The maximum value any entry in the Hough transform can take.
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
 
means(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(double[]) - Method in class registration.SearchMI
Compute the mutual information of images a and (b transformed according to p).
mi(float[]) - Method in class registration.SearchMI
Compute the mutual information of images a and (b transformed according to p).
mi(float[], float[]) - Method in class bijnum.BIJmi
 
mi(float[], float[], int, float[][]) - Method in class registration.SearchMI
Compute mutual information of the common parts of the transformation of image b and a.
mi(short[], short[]) - Method in class bijnum.BIJmi
 
midPointStep(DoubleArrayParametrized, DoubleArrayValued, double[], double[], double, int, double[], double[], double[]) - Static method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
miLight - Variable in class VolumeJ.VJRenderer
Separate transformation matrix and inverse for the light.
milneSum(double[]) - Static method in class numericalMethods.calculus.integration.NewtonCotes
 
min - Variable in class bijnum.BIJmi
 
min - Variable in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
MIN_LINE_COS_ANGLE - Static variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
min() - Method in class FlowJ.SSD
 
min(int[]) - Static method in class stereodisk.StereoDiskAnalyzer
 
min(int[]) - Static method in class stereodisk.StereoDiskIxConverter
 
min(int, int, float[][], int[][]) - Method in class FlowJ.FlowJUras
 
minCond(int[][], float[][], int) - Method in class FlowJ.FlowJUras
 
minimize(double[], int[], int[], double, int, double) - Static method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
minimize(double[], int[], int[], int, double) - Static method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
minimize(double[], int[], int[], int, int, double) - Static method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
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
 
minmaxref - Variable in class registration.RegisterMI
 
minMI - Variable in class registration.SearchMI
 
minp - Variable in class registration.SearchMI
 
minPower2(int) - Static method in class bijnum.BIJutil
Find the minimal power of 2 that is larger than n.
minus(double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A - B = C .
minus(double[][], double, double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A - b = C .
minus(double[][], int[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A - B = C.
minus(double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a - b = c.
minus(double[], double, double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a - b = c .
minus(double[], int[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a - b = c .
minus(double, double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
performs: a - B = C .
minus(double, double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a - b = c.
minus(int[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A - B = C .
minus(int[][], double, double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A - b = C .
minus(int[][], int[][], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A - B = C.
minus(int[][], int, int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A - b = C .
minus(int[], double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a - b = c.
minus(int[], int[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a - b = c .
minus(int[], int, int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a - b = c .
minus(int, double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A - B = C .
minus(int, int[][], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: a - B = C .
minus(int, int[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a - b = c .
minus(Matrix) - Method in class Jama.Matrix
C = A - B
minusEquals(Matrix) - Method in class Jama.Matrix
A = A - B
mLight - Variable in class VolumeJ.VJRenderView
State variables.
mLight - Variable in class VolumeJ.VJRenderer
Separate transformation matrix and inverse for the light.
mod(int[][], int, int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs A % b = C.
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.
mousePressed(MouseEvent) - Method in class retina.OIDCanvas
 
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.
msFrameDurationPhase1 - Variable in class va.TimedAcquisition
 
msFrameDurationPhase2 - Variable in class va.TimedAcquisition
 
msPhase1End - Variable in class va.TimedAcquisition
 
msPhase2End - Variable in class va.TimedAcquisition
 
mu - Static variable in class numericalMethods.geometry.latticeReduction.LLL
 
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.
multipleFiles - Static variable in class retina.EpochSorter
 
multiplyToConst(double, double, double[], double[], int, double[], double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
This methods multiplies a complex polynomial with constant complex number.

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 number of different classes in classset.
n - Variable in class bijnum.BIJmi
 
n - Variable in class bijnum.BIJJacobi
 
n - Variable in class bijnum.BIJfft
Local variables used in BIJfht algorithms.
n - Variable in class knn.FilterBank
 
n - Variable in class knn.StereoFilterBank
 
n - Variable in class numericalMethods.calculus.minimizing.NumericalGradient
 
n - Variable in class numericalMethods.calculus.minimizing.nmLineND
 
n - Variable in class numericalMethods.calculus.minimizing.Quadric
 
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
 
n2 - Variable in class bijnum.BIJfft
Local variables used in BIJfht algorithms.
name - Variable in class knn.Feature
 
name - Variable in class retina.OIDHeader
 
name - Variable in class retina.RTA_Thickness_Reader
 
name - Variable in class retina.RTA_Reader
 
name(double, double, double, String) - Static method in class knn.StereoFilterBank
 
name(double, double, double, String) - Static method in class knn.DOGFilterBank
 
name(int) - Static method in class knn.FeatureComputer
 
name(int, double, double, String) - Static method in class knn.FilterBank
 
names - Variable in class io.OpenPreviewDialog
The names of the files that were selected, null if no selection.
ndf - Variable in class numericalMethods.calculus.minimizing.Quadric
 
NEG_POS - Static variable in class numericalMethods.algebra.loopGroup.BirkhoffFactorization
 
neg(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Negates matrix A and stores result in B .
neg(double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Negates vector a and stores result in b.
neg(int[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Negates matrix A and stores result in B .
neg(int[][], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Negates matrix A and stores result in B .
neg(int[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Negates vector a and stores result in b.
neg(int[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Negates vector a and stores result in b.
neighbor - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
net.sourceforge.jannealer - package net.sourceforge.jannealer
 
net.sourceforge.jannealer.test - package net.sourceforge.jannealer.test
 
newEdge - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
newFace - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
newMatrix(int) - Static method in class bijnum.BIJtransform
Create a new (diagonal) transformation matrix for the number of dimensions.
NewtonCotes - class numericalMethods.calculus.integration.NewtonCotes.
 
NewtonCotes() - Constructor for class numericalMethods.calculus.integration.NewtonCotes
 
NewtonRaphson - class numericalMethods.calculus.rootFinding.NewtonRaphson.
Newton-Raphson method's for finding roots of real and complex functions.
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
 
next(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Replaces a permutation with the next permutation in the cyclic lexicographic order.
nextDerangement(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Replaces a derangement (permutation with no fixed point) with the next derangement in the cyclic lexicographic order.
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.
nf - Variable in class numericalMethods.calculus.minimizing.Quadric
 
niceCopy() - Method in class retina.OIDWindow
 
nilFixedPoints(double[]) - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
nIterations - Variable in class net.sourceforge.jannealer.AnnealingScheme
 
nmBracket - class numericalMethods.calculus.minimizing.nmBracket.
 
nmBracket() - Constructor for class numericalMethods.calculus.minimizing.nmBracket
 
nmBrent - class numericalMethods.calculus.minimizing.nmBrent.
 
nmBrent() - Constructor for class numericalMethods.calculus.minimizing.nmBrent
 
nmDoubleArrayParametrized - interface numericalMethods.function.nmDoubleArrayParametrized.
Interface for objects that represent functions of a double array parameter.
nmDoubleArrayValued - interface numericalMethods.function.nmDoubleArrayValued.
Interface for objects that represent double array valued functions.
nmDoubleParametrized - interface numericalMethods.function.nmDoubleParametrized.
Interface for objects that represent functions of a double parameter.
nmDoubleValued - interface numericalMethods.function.nmDoubleValued.
Interface for objects that represent double valued functions.
nmLineND - class numericalMethods.calculus.minimizing.nmLineND.
 
nmLineND(double[], double[]) - Constructor for class numericalMethods.calculus.minimizing.nmLineND
 
nmLineNDBrent - class numericalMethods.calculus.minimizing.nmLineNDBrent.
 
nmLineNDBrent(nmDoubleArrayParametrized, nmDoubleValued) - Constructor for class numericalMethods.calculus.minimizing.nmLineNDBrent
 
nmLineNDBrent(nmDoubleArrayParametrized, nmDoubleValued, double[], double[]) - Constructor for class numericalMethods.calculus.minimizing.nmLineNDBrent
 
nmLineNDEvaluator - class numericalMethods.calculus.minimizing.nmLineNDEvaluator.
 
nmLineNDEvaluator(nmDoubleArrayParametrized) - Constructor for class numericalMethods.calculus.minimizing.nmLineNDEvaluator
 
nmLineNDEvaluator(nmDoubleArrayParametrized, nmDoubleValued) - Constructor for class numericalMethods.calculus.minimizing.nmLineNDEvaluator
 
nmLineNDEvaluator(nmDoubleArrayParametrized, nmDoubleValued, double[], double[]) - Constructor for class numericalMethods.calculus.minimizing.nmLineNDEvaluator
 
nmPowell - class numericalMethods.calculus.minimizing.nmPowell.
 
nmPowell() - Constructor for class numericalMethods.calculus.minimizing.nmPowell
 
no - Variable in class VolumeJ.VJOutlineShader
The outline exponent.
nob - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
nodes - Variable in class bd.BDSeparatorLattice
 
nof - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer
 
nof - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
noiseAnalysis(float[][], int, int, float[][], int) - Static method in class retina.OIDAnalysis
Analysis of noise in a without masks.
nonlinear(float[], double) - Static method in class volume.Convolver
Deprecated.  
noo - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
nop - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
norm(float[]) - Static method in class bijnum.BIJmatrix
Return length or norm of vector v.
norm1() - Method in class Jama.Matrix
One norm
norm2() - Method in class Jama.SingularValueDecomposition
Two norm
norm2() - Method in class Jama.Matrix
Two norm
normalize() - Method in class VolumeJ.VJGradient
 
normalize() - Method in class of3d.OF3DFlow
 
normalize(double[][][], double[][][], double[][][], double[][][], double[][], double[][], double[][], double[][], double[], double[], double[], double[], boolean, boolean) - Static method in class numericalMethods.algebra.loopGroup.BirkhoffFactorization
 
normalize(float[], double) - Static method in class volume.Convolver
Deprecated.  
normals(float, float) - Method in class FlowJ.FlowJFleet
 
normF() - Method in class Jama.Matrix
Frobenius norm
normInf() - Method in class Jama.Matrix
Infinity norm
normSqr(double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
 
normSqr(double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Return the sum of the squares of all entries.
normSqr(int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
 
normSqr(int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Return the sum of the squares of all entries.
notOpaque() - Method in class VolumeJ.VJAlphaColor
 
nrclasses - Static variable in class stereodisk.StereoDiskANNTester
 
nrclasses - Static variable in class stereodisk.StereoDiskROC
 
nrFrames - Variable in class retina.OIDProcessor
Counter for number of frames.
nrImages - Static variable in class retina.OIDtc
 
nrIndexBits - Variable in class VolumeJ.VJClassifierLevoy
 
nrIntensityBits - Variable in class VolumeJ.VJClassifierLevoy
 
nrMagnitudeBits - Variable in class VolumeJ.VJClassifierLevoy
 
nrOrders - Variable in class knn.FilterBank
 
nrOrders - Variable in class knn.StereoFilterBank
 
nrot - Variable in class bijnum.BIJJacobi
 
nrot() - Method in class bijnum.Jacobi
Deprecated.  
nrot() - Method in class bijnum.BIJJacobi
 
NRSLICES - Static variable in class retina.OIDHeader
 
nrSuspectRegistrations - Variable in class retina.OIDProcessor
Counter for suspect registrations.
nrUniqueConditions - Variable in class retina.OIDProcessor
Other parameters describing the layout of aggregate.
nseq - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
ntestpixels - Static variable in class stereodisk.StereoDiskANNTester
 
ntestpixels - Static variable in class stereodisk.StereoDiskROC
 
ntrainpixels - Static variable in class stereodisk.StereoDiskANNTester
 
ntrainpixels - Static variable in class stereodisk.StereoDiskROC
 
nu - Variable in class bijnum.BIJfft
Local variables used in BIJfht algorithms.
nu1 - Variable in class bijnum.BIJfft
Local variables used in BIJfht algorithms.
number - Static variable in class VolumeJ.VJUserInterface
 
numberOfUniqueStrings(String[]) - Static method in class retina.EpochSorter
Return the number of unique strings in s.
NumericalGradient - class numericalMethods.calculus.minimizing.NumericalGradient.
 
NumericalGradient(DoubleValued) - Constructor for class numericalMethods.calculus.minimizing.NumericalGradient
 
NumericalGradient(DoubleValued, double) - Constructor for class numericalMethods.calculus.minimizing.NumericalGradient
 
numericalMethods - package numericalMethods
The package numericalMethods is a collection of mostly standard routines providing numerical solutions for many common problems in algebra, calculus, and geometry.
numericalMethods.algebra - package numericalMethods.algebra
The algebra branch of numericalMethods.
numericalMethods.algebra.group - package numericalMethods.algebra.group
 
numericalMethods.algebra.linear - package numericalMethods.algebra.linear
Algorithms related to linear algebra.
numericalMethods.algebra.linear.decompose - package numericalMethods.algebra.linear.decompose
Algorithms related to decomposition of matrices and their determinants.
numericalMethods.algebra.linear.solve - package numericalMethods.algebra.linear.solve
Algorithms related to solving of linear equation systems.
numericalMethods.algebra.loopGroup - package numericalMethods.algebra.loopGroup
 
numericalMethods.algebra.polynomial - package numericalMethods.algebra.polynomial
Algorithms related to polynomials.
numericalMethods.calculus - package numericalMethods.calculus
The calculus branch of numericalMethods.
numericalMethods.calculus.functionApproximation - package numericalMethods.calculus.functionApproximation
Algorithms for function approximation.
numericalMethods.calculus.integration - package numericalMethods.calculus.integration
Algorithms for numerical integration.
numericalMethods.calculus.minimizing - package numericalMethods.calculus.minimizing
Implementations for minimizing functional objects.
numericalMethods.calculus.odeSolving - package numericalMethods.calculus.odeSolving
Algorithms for solving ordinary differential equations.
numericalMethods.calculus.rootFinding - package numericalMethods.calculus.rootFinding
Implementations for root finding of functional objects.
numericalMethods.calculus.specialFunctions - package numericalMethods.calculus.specialFunctions
Implementations of special functions.
numericalMethods.function - package numericalMethods.function
Interfaces describing functional objects.
numericalMethods.function.util - package numericalMethods.function.util
Utilities related to interfaces for functional objects.
numericalMethods.geometry - package numericalMethods.geometry
The geomtry branch of numericalMethods.
numericalMethods.geometry.bounding - package numericalMethods.geometry.bounding
 
numericalMethods.geometry.hyperSurface - package numericalMethods.geometry.hyperSurface
 
numericalMethods.geometry.latticeReduction - package numericalMethods.geometry.latticeReduction
Implementations of lattice reduction algorithms.
numericalMethods.geometry.meshGeneration - package numericalMethods.geometry.meshGeneration
 
numericalMethods.geometry.meshGeneration.ruppert - package numericalMethods.geometry.meshGeneration.ruppert
 
numericalMethods.geometry.meshGeneration.util - package numericalMethods.geometry.meshGeneration.util
 
numericalMethods.util - package numericalMethods.util
Miscellaneous routines and utilities.
numInversions(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Each permutation can be written as a product of transpositions of consecutive elements.
numOfElements - Variable in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
numOfEquations - Variable in class numericalMethods.calculus.odeSolving.RungeKutta
 
numOfEquations - Variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
numOfEquations - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
numOfEvaluations - Variable in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
numOfKeys - Variable in class numericalMethods.function.util.AbstractValueCacher
 
numOfPoints - Variable in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
numTranspos(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Each permutation can be written as a product of transpositions.
numTranspos(int[], boolean[]) - Static method in class numericalMethods.algebra.group.Permutation
Describe numTranspos method here.
numTranspos(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Same as Permutation.numTranspos(int[]) but uses a preinstanciated int[] of length at least the length of p.

O

objectify(VJMatrix) - Method in class VolumeJ.VJLight
Transform the position of this light into another coordinate system.
ObjectiveFunction - interface net.sourceforge.jannealer.ObjectiveFunction.
This interface must be implemented by all the classes that encapsulate a function that is to be minimized
obsolete - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
odeSolver - Variable in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
OdeSolver - interface numericalMethods.calculus.odeSolving.OdeSolver.
 
OdeSolverBasedIntegrator - class numericalMethods.calculus.integration.OdeSolverBasedIntegrator.
 
OdeSolverBasedIntegrator(OdeSolver) - Constructor for class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double) - Method in class numericalMethods.calculus.odeSolving.RungeKutta
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double) - Method in interface numericalMethods.calculus.odeSolving.OdeSolver
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double) - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double) - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double, double[], double[], double[], int, DoubleArrayValued) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double, double[], double, double) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double, double[], double, double, DoubleArrayValued) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double, double[], double, int[], DoubleArrayParametrized, BulirschStoer.TempDataContainer) - Static method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double, double, double[], double, int[], DoubleArrayParametrized) - Static method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double, double, double[], double, int[], DoubleArrayParametrized) - Static method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
odex(DoubleArrayParametrized, DoubleArrayValued, double[], double, double, double[], double, int[], DoubleArrayParametrized, double[][]) - Static method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
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
 
offset - Variable in class net.sourceforge.jannealer.AnnealingScheme
 
OFXYZ - Static variable in class of3d.OF3DUserInterface
 
OFXZY - Static variable in class of3d.OF3DUserInterface
 
OFYZX - Static variable in class of3d.OF3DUserInterface
 
OIDamplitudeAnalyzer - class retina.OIDamplitudeAnalyzer.
Analysis of the reflectance signal in terms of the amplitude at a certain moment.
OIDamplitudeAnalyzer(ScriptProcessor) - Constructor for class retina.OIDamplitudeAnalyzer
 
OIDAnalysis - class retina.OIDAnalysis.
Optical Imaging frame sequence analysis.
OIDAnalysis() - Constructor for class retina.OIDAnalysis
 
OIDAnalyzer - class retina.OIDAnalyzer.
Optical Imaging of the Retina first frame analyzer.
OIDAnalyzer() - Constructor for class retina.OIDAnalyzer
 
OIDAnalyzer(ScriptProcessor) - Constructor for class retina.OIDAnalyzer
 
OIDAverageAnalyzer - class retina.OIDAverageAnalyzer.
Optical Imaging of the Retina first frame analyzer.
OIDAverageAnalyzer() - Constructor for class retina.OIDAverageAnalyzer
 
OIDAverageAnalyzer(ScriptProcessor) - Constructor for class retina.OIDAverageAnalyzer
 
OIDBaseAnalyzer - interface retina.OIDBaseAnalyzer.
Is the abstract interface definition for all OID Analyzers.
OIDbaselineAnalyzer - class retina.OIDbaselineAnalyzer.
Optical Imaging of the Retina baseline frame analyzer.
OIDbaselineAnalyzer() - Constructor for class retina.OIDbaselineAnalyzer
 
OIDbaselineAnalyzer(ScriptProcessor) - Constructor for class retina.OIDbaselineAnalyzer
 
OIDCanvas - class retina.OIDCanvas.
User interface for optical imaging sequences.
OIDCanvas(ImagePlus) - Constructor for class retina.OIDCanvas
 
OIDffAllAnalyzer - class retina.OIDffAllAnalyzer.
Optical Imaging of the Retina first frame analyzer for all frames (not only stimulus frames) but average across conditions.
OIDffAllAnalyzer() - Constructor for class retina.OIDffAllAnalyzer
 
OIDffAllAnalyzer(ScriptProcessor) - Constructor for class retina.OIDffAllAnalyzer
 
OIDHeader - class retina.OIDHeader.
Defines the header for KES/DAT files for OID devices.
OIDHeader() - Constructor for class retina.OIDHeader
 
OIDHeader(byte[], String) - Constructor for class retina.OIDHeader
Instantiates an OIDHeader from known header bytes (in .kes file) and String from .dat file.
OIDHeader(File) - Constructor for class retina.OIDHeader
Instantiates an OIDHeader from a .dat File.
OIDHeader(int, int, int, String) - Constructor for class retina.OIDHeader
Instantiates an OIDHeader from image file parameters and properly formatted String headerInfo.
OIDHeader(String, String) - Constructor for class retina.OIDHeader
Instantiates an OIDHeader from both .kes and .dat files.
OIDMapsFitter - class retina.OIDMapsFitter.
Fits stimulus map stacks into retinal reflectance images.
OIDMapsFitter() - Constructor for class retina.OIDMapsFitter
 
OIDMapsFitter(ScriptProcessor) - Constructor for class retina.OIDMapsFitter
 
OIDPCAAnalyzer - class retina.OIDPCAAnalyzer.
Does PCA analysis on OID files.
OIDPCAAnalyzer() - Constructor for class retina.OIDPCAAnalyzer
 
OIDPCAAnalyzer(ScriptProcessor) - Constructor for class retina.OIDPCAAnalyzer
 
OIDProcessor - class retina.OIDProcessor.
Optical Imaging frame sequence analysis.
OIDProcessor() - Constructor for class retina.OIDProcessor
Start an OIDProcessor.
OIDProcessor(FileInfo, String[]) - Constructor for class retina.OIDProcessor
Start an OIDProcessor for the FileInfo fi and epochNames, an array of file names.
OIDReconstructor - class retina.OIDReconstructor.
OID reconstructor with directory navigation.
OIDReconstructor(String, Object, String) - Constructor for class retina.OIDReconstructor
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.
OIDroiAnalyzer - class retina.OIDroiAnalyzer.
Does ROI analysis of OID files.
OIDroiAnalyzer() - Constructor for class retina.OIDroiAnalyzer
 
OIDroiAnalyzer(ScriptProcessor) - Constructor for class retina.OIDroiAnalyzer
 
OIDroiTCAnalyzer - class retina.OIDroiTCAnalyzer.
Does ROI analysis of OID files and looks for timecourse of all different possible stimuli.
OIDroiTCAnalyzer() - Constructor for class retina.OIDroiTCAnalyzer
 
OIDroiTCAnalyzer(ScriptProcessor) - Constructor for class retina.OIDroiTCAnalyzer
 
OIDROItimecourseAnalyzer - class retina.OIDROItimecourseAnalyzer.
Optical Imaging of the Retina timecourse analyzer.
OIDROItimecourseAnalyzer() - Constructor for class retina.OIDROItimecourseAnalyzer
 
OIDStackWindow - class retina.OIDStackWindow.
Optical Imaging frame sequence analysis.
OIDStackWindow(ImagePlus) - Constructor for class retina.OIDStackWindow
Start an OIDProcessor for imp.
OIDStackWindow(ImagePlus, ImageCanvas, FileInfo, String[]) - Constructor for class retina.OIDStackWindow
Start an OIDProcessor for imp.
OIDtc - class retina.OIDtc.
Does truncated differencing on existing PCA files.
OIDtc() - Constructor for class retina.OIDtc
 
OIDTimecourseAnalyzer - class retina.OIDTimecourseAnalyzer.
Optical Imaging of the Retina timecourse analyzer for all frames (not only stimulus frames).
OIDTimecourseAnalyzer() - Constructor for class retina.OIDTimecourseAnalyzer
 
OIDTimecourseAnalyzer(ScriptProcessor) - Constructor for class retina.OIDTimecourseAnalyzer
 
OIDTimecourseStimulatedAnalyzer - class retina.OIDTimecourseStimulatedAnalyzer.
Optical Imaging of the Retina timecourse analyzer.
OIDTimecourseStimulatedAnalyzer() - Constructor for class retina.OIDTimecourseStimulatedAnalyzer
 
OIDTimecourseStimulatedAnalyzer(ScriptProcessor) - Constructor for class retina.OIDTimecourseStimulatedAnalyzer
 
OIDWindow - class retina.OIDWindow.
Optical Imaging frame sequence analysis.
OIDWindow(ImagePlus, ImageCanvas, FileInfo, String[]) - Constructor for class retina.OIDWindow
Start an OIDWindow for imp.
OLD - Static variable in class bd.BlobDetector
 
oldies - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
onlyStim - Variable in class retina.OIDWindow
 
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
 
open(String) - Method in class retina.RTA_Thickness_Reader
Opens the specified RTA map and process thickness array.
open(String) - Method in class retina.RTA_Reader
Opens the specified text file as a float image.
opening - Variable in class retina.OIDReconstructor
 
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 - Static variable in class retina.EpochSorter
 
order - Variable in class volume.GaussianDerivative
 
order(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the order of the given permutation.
order(int[], boolean[]) - Static method in class numericalMethods.algebra.group.Permutation
Describe order method here.
order(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Same as Permutation.order(int[]) but uses a preinstanciated int[] of length at least the length of p.
order7Sum(double[]) - Static method in class numericalMethods.calculus.integration.NewtonCotes
 
order9Sum(double[]) - Static method in class numericalMethods.calculus.integration.NewtonCotes
 
org.theblueplanet.annealing - package org.theblueplanet.annealing
 
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
 
OUTPUTTAG - Static variable in class retina.ScriptProcessor
 
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
 
p - Variable in class registration.SearchMI
The parameters that can be set by setDoubleArrayParameter.
paint(Graphics) - Method in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DrawingPanel
 
paint(Graphics) - Method in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel
 
panel - Variable in class io.OpenPreviewDialog
 
parameters - Variable in class retina.ScriptProcessor
Contains the parameters that can be set.
parameterStrings - Variable in class retina.ScriptProcessor
Contains the parameters that can be set.
params() - Method in class volume.Diffusion
 
params(ImagePlus, VolumeFloat) - Method in class volume.Diffusion3D
 
params(int) - Method in class knn.FilterBank
Determine the order, scale and orientation of a numbered filter.
params(int) - Method in class knn.StereoFilterBank
Determine the order, scale and orientation of a numbered filter.
params4D(ImagePlus) - Method in class volume.Diffusion3D
 
parity(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Gives the parity of the number of transpositions.
parse(Reader) - Static method in class retina.EpochSorter
Parse the stream r, looking for
parse(Reader, Hashtable) - Method in class retina.ScriptProcessor
Parse the stream r, looking for parameters in dictionary.
path - Variable in class retina.RTA_Thickness_Reader
 
path - Variable in class retina.RTA_Reader
 
pca - Variable in class retina.PCAWindow
 
pca - Variable in class retina.OIDWindow
 
PCAWindow - class retina.PCAWindow.
Window to do various types of PCA analysis.
PCAWindow(ImagePlus, ImageCanvas, BIJpca) - Constructor for class retina.PCAWindow
Create an extended PCA window from a StackWindow.
peak(int, int) - Method in class FlowJ.SSD
 
peakloc - Variable in class FlowJ.SSD
 
peakMag() - Static method in class bijfit.Maximum
 
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.
perform(AWTEvent) - Method in class va.VAInterface
Actual processing.
Permutation - class numericalMethods.algebra.group.Permutation.
Permutation.java
Permutation() - Constructor for class numericalMethods.algebra.group.Permutation
 
permutation(int) - Method in class VolumeJ.VJMatrix
Make a permutation for one of the major axes (x,y,z) Used for shear-warp rendering.
PGROW - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
PGROW - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
phi - Variable in class bijnum.BIJgifa
 
pimp - Variable in class retina.PCAWindow
 
PIXEL_SAMPLING - Static variable in class stereodisk.StereoDiskAnalyzer
 
PIXEL_SAMPLING - Static variable in class stereodisk.StereoDiskIxConverter
 
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.
pixelsField - Variable in class bd.BDUserInterface
 
pixelSize - Variable in class VolumeJ.VJViewspaceRender
size of entry viewspacePixel.
pixelsToDataset(float[][][]) - Static method in class stereodisk.StereoDiskAnalyzer
samplePixels contains the pixel values for each sampled image for each feature (N).
plotParameters(String, float[][]) - Static method in class registration.Register
Plot the parameters in various PlotWindows.
plotProbs(float[][], Vector, String, String) - Static method in class stereodisk.StereoDiskAnalyzer
Plot the probabilities for each feature.
PLR - class numericalMethods.algebra.linear.decompose.PLR.
Computes for a square matrix A the matrices P, L and R complying P·A=L·R.
PLR() - Constructor for class numericalMethods.algebra.linear.decompose.PLR
 
plus(double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A + B = C.
plus(double[][], double, double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A + b = C .
plus(double[][], int[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A + B = C .
plus(double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a + b = c.
plus(double[], double[], int, double[], double[], int, double[], double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
plus(double[], double, double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a + b = c .
plus(double[], int[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a + b = c.
plus(int[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A + B = C .
plus(int[][], double, double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A + b = C .
plus(int[][], int[][], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A + B = C .
plus(int[][], int, int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs: A + b = C .
plus(int[], double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a + b = c.
plus(int[], int[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a + b = c.
plus(int[], int, int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs a + b = c.
plus(Matrix) - Method in class Jama.Matrix
C = A + B
plusEquals(Matrix) - Method in class Jama.Matrix
A = A + B
point - Variable in class numericalMethods.calculus.minimizing.nmLineND
 
point - Variable in class numericalMethods.calculus.minimizing.Quadric
 
point - Variable in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
point - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer
 
point - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
pointAtT - Variable in class numericalMethods.calculus.minimizing.nmLineNDEvaluator
 
pointInCircle(double, double, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
pointInFace(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
pointIsFix - Variable in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
pointIsFix(int[], int[], int) - Static method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
pointOnEdge - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
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
 
poly(float[], float[]) - Static method in class bijnum.BIJfit
Given a line with points x, y, fit a line y = bx + a through them with linear least squares regression.
polynomialExtrapolation(int, double, double[], double[], double[], double[], double[], double[][]) - Static method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
POS_NEG - Static variable in class numericalMethods.algebra.loopGroup.BirkhoffFactorization
 
positivePart(double[][][], double[][][], double[][][], double[][][], double[][][], double[][][]) - Static method in class numericalMethods.algebra.loopGroup.IwasawaFactorization
Matrix Laurent series multiplication b = star(f) * x Assumes degrees f: (-N, N), x: (-N, N), b: (0, N) Used to compute the positive part of the factorization.
positivePart(double[][][], double[][][], double[][][], double[][][], double[][][], double[][][], double[], double[]) - Static method in class numericalMethods.algebra.loopGroup.IwasawaFactorization
 
postprocess(float[][]) - Static method in class stereodisk.StereoDiskFeatureConverter
Postprocess the feature images.
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.
precessor - Variable in class numericalMethods.function.util.AbstractValueCacher.Key
 
precision - Variable in class registration.RegisterMI
 
preDefinedOrder - Static variable in class retina.EpochSorter
 
prefersRegistration() - Method in class retina.OIDAnalyzer
 
prefersRegistration() - Method in class retina.OIDTimecourseAnalyzer
 
prefersRegistration() - Method in class retina.OIDTimecourseStimulatedAnalyzer
 
prefersRegistration() - Method in class retina.OIDMapsFitter
 
prefersRegistration() - Method in class retina.OIDroiAnalyzer
 
prefersRegistration() - Method in class retina.OIDPCAAnalyzer
 
prefersRegistration() - Method in class retina.OIDROItimecourseAnalyzer
 
prefersRegistration() - Method in interface retina.OIDBaseAnalyzer
 
prepare(float, float, int) - Method in class of3d.OF3DLucas
 
previous(int[]) - Static method in class numericalMethods.algebra.group.Permutation
The previous one in the lexicographic order.
print(int, int) - Method in class Jama.Matrix
Print the matrix to stdout.
print(NumberFormat, int) - Method in class Jama.Matrix
Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class Jama.Matrix
Print the matrix to the output stream.
print(PrintWriter, NumberFormat, int) - Method in class Jama.Matrix
Print the matrix to the output stream.
printInfo() - Static method in class retina.OIDAnalyzer
 
printInfo() - Method in class retina.OIDMapsFitter
 
printInfo() - Method in class retina.OIDroiAnalyzer
 
printInfo() - Method in class retina.OIDroiTCAnalyzer
 
printInfo() - Method in class retina.OIDPCAAnalyzer
 
printInfo() - Method in class retina.OIDamplitudeAnalyzer
 
printInfo() - Method in class retina.OIDROItimecourseAnalyzer
 
printSolution(AnnealingScheme) - Static method in class net.sourceforge.jannealer.test.Util
dump solution to screen
printStatistics() - Method in class numericalMethods.calculus.odeSolving.Extrap
 
printUsage() - Static method in class retina.OIDAnalyzer
 
process() - Method in class retina.ScriptProcessor
Process the OID files.
process(float[][][], float[][][][], String, String, String[]) - Method in class retina.OIDTimecourseAnalyzer
process r results.
processAverageResults(float[][], String, int, int, float[][], float[][], float[][], int) - Method in class retina.OIDTimecourseAnalyzer
 
processor - Variable in class retina.OIDStackWindow
 
processPDSresults(double[][], double[][], String) - Method in class retina.OIDTimecourseAnalyzer
Process an array of PDS results and its frequencies.
processToString(String) - Static method in class stereodisk.StereoDiskPGMConverter
 
progress(double) - Method in class bijnum.BIJfht
Can be used to show progress in other programs.
progress(double) - Method in class bijnum.BIJfft
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.
propertyChangeSupport - Variable in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
propertyChangeSupport - Variable in class numericalMethods.calculus.odeSolving.RungeKutta
 
propertyChangeSupport - Variable in class numericalMethods.calculus.odeSolving.Extrap
 
propertyChangeSupport - Variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
propertyChangeSupport - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
prune(int) - Method in class bijnum.BIJknn
Cleans the dataset using Wilson's pruning algorithm.
pruneMax() - Method in class net.sourceforge.jannealer.SimplexList
Remove from list.
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.  
PSHRNK - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
PSHRNK - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
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
 
putAveragesAtEnd(float[][], int, int) - Static method in class retina.OIDAnalysis
Compute the average of each group of n vectors (there are n groups) of length length in a into the length+1 vector in a.
putHeaderAsString(File) - Method in class retina.OIDHeader
Writes the header text as a String to the appropriate file
Puv - Variable in class bijnum.BIJmi
 
Pv - Variable in class bijnum.BIJmi
 

Q

q - Static variable in class FlowJ.FlowJSpotNoise
 
QR - class numericalMethods.algebra.linear.decompose.QR.
Computes for a square matrix A the matrices Q and R complying A=Q·R.
qr() - Method in class Jama.Matrix
QR Decomposition
QR() - Constructor for class numericalMethods.algebra.linear.decompose.QR
 
QRDecomposition - class Jama.QRDecomposition.
QR Decomposition.
QRDecomposition(Matrix) - Constructor for class Jama.QRDecomposition
QR Decomposition, computed by Householder reflections.
qScaling - Variable in class FlowJ.FlowJMapper
 
qTimes(double[][], double[][], boolean, double[]) - Static method in class numericalMethods.algebra.linear.decompose.Householder
Computes the product of a matrix with the producing vectors of an orthogonal matrix and a matrix.
qTimes(double[][], double[][], double[][], double[][], boolean, double[], double[]) - Static method in class numericalMethods.algebra.linear.decompose.Householder
Computes the product of a matrix with the producing vectors of an unitary matrix with a matrix.
qTimes(double[][], double[][], double[], double[], boolean) - Static method in class numericalMethods.algebra.linear.decompose.Householder
Computes the product of a matrix with the producing vectors of an unitary matrix with a vector.
qTimes(double[][], double[], boolean) - Static method in class numericalMethods.algebra.linear.decompose.Householder
Computes the product of a matrix with the producing vectors of an orthogonal matrix and a vector.
Quadric - class numericalMethods.calculus.minimizing.Quadric.
 
Quadric(int) - Constructor for class numericalMethods.calculus.minimizing.Quadric
 
quick(float[], int, int, int) - Static method in class volume.Transformer
Quickly transform an image for whole pixel shifts.
quitB - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel
 
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
 
R - Static variable in class numericalMethods.calculus.minimizing.Golden
 
radius - Variable in class registration.LocatedCircle
 
radius - Variable in class registration.HoughTransform
 
ran1(long) - Static method in class net.sourceforge.jannealer.RandomUtil
Adapted from Numerical Recipes in C 'Minimal' random number generator Call with idum negative to initialize
random - Variable in class of3d.FlowJValue
 
random(double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Assigns random all entries of v.
random(double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns random all entries of m.
random(int) - Static method in class numericalMethods.algebra.group.Permutation
Returns a random permutation on the letters 0..len-1.
random(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Replaces the parameter array with a random array on the letters 0..len-1 where len=s.length.
random(int[][], int) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Assigns random all entries of m.
random(int[], int) - Static method in class numericalMethods.algebra.group.Permutation
Replaces the parameter array with a random array on the letters 0..len-1 where len=s.length.
random(int[], int) - Static method in class numericalMethods.algebra.linear.VectorOperations
Assigns random all entries of v.
random(int, int) - Static method in class Jama.Matrix
Generate matrix with random elements
random(int, int) - Static method in class numericalMethods.algebra.group.Permutation
Returns a random permutation on the letters 0..len-1.
randomblock - Variable in class retina.ScriptProcessor
May contain permuted random block for stimulus conditions.
randomFraction(float[], double) - Static method in class bijnum.BIJstats
Randomly sample a fraction of the elements of vector v.
RandomUtil - class net.sourceforge.jannealer.RandomUtil.
Returns randomly distributed numbers (white distribution) over a specified interval for 4 specified types: int, long, float & double
RandomUtil() - Constructor for class net.sourceforge.jannealer.RandomUtil
 
rank() - Method in class Jama.SingularValueDecomposition
Effective numerical matrix rank
rank() - Method in class Jama.Matrix
Matrix rank
RAW_OFFSET - Static variable in class retina.OIDHeader
 
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(BufferedReader) - Static method in class Jama.Matrix
Read a matrix from a stream.
read(Reader, String) - Static method in class retina.RTAReader
Parser for RTA files.
read(String) - Method in class FlowJ.FlowJFlow
Read a flow field defined in a file.
read(String) - Method in class of3d.OF3DFlow
 
REALEDGEFRACTION - Static variable in class retina.RetinalImage
Fraction of edge histogram pixels that are real edges.
recompute(float) - Method in class FlowJ.SSD
 
Reconstructors - package Reconstructors
 
REDMAX - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
REDMIN - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
reduce(double[][]) - Static method in class numericalMethods.geometry.latticeReduction.LLL
 
reduce(double[][], double[][]) - Static method in class numericalMethods.geometry.latticeReduction.LLL
 
reduce(double[][], int[][]) - Static method in class numericalMethods.geometry.latticeReduction.LLL
 
reduce(double[][], int[][], double[][], double) - Static method in class numericalMethods.geometry.latticeReduction.LLL
 
reduce(long[][], long[][]) - Static method in class numericalMethods.geometry.latticeReduction.ExactLLL
 
reduce(long[][], long[][], long[]) - Static method in class numericalMethods.geometry.latticeReduction.ExactLLL
 
reduce(long[][], long[][], long, long, long[]) - Static method in class numericalMethods.geometry.latticeReduction.ExactLLL
 
reduce(long[][], long, long, long[]) - Static method in class numericalMethods.geometry.latticeReduction.ExactLLL
 
reference - Variable in class registration.Register
The reference image.
referenceDisk - Variable in class registration.RegisterRetina
 
referencefft - Variable in class registration.RegisterFFTHessian
 
referencefft - Variable in class registration.RegisterFFT
 
refine() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
refine(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
refineB - Variable in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer.DelaunayPanel
 
refineFlag - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
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.
Register - class registration.Register.
Top class for all registration implementations.
Register() - Constructor for class registration.Register
 
register(float[]) - Method in class registration.Register
 
register(float[]) - Method in class registration.RegisterFFTHessian
Register the image in a to the reference image.
register(float[]) - Method in class registration.RegisterMI
Register the image in a to the reference image using MI.
register(float[]) - Method in class registration.RegisterFFT
Register the image in a to the reference image.
register(float[]) - Method in class registration.RegisterRetina
Register the image a to the reference image.
registerEpoch(Register, ImagePlus, float[][], int, float[], int) - Method in class retina.OIDProcessor
Register the frames in the k'th epoch (in epochimp) to reference.
RegisterFFT - class registration.RegisterFFT.
Registration using Fourier transform cross-correlation.
RegisterFFT(float[], int) - Constructor for class registration.RegisterFFT
Prepare for registration including preprocessing of the reference image.
RegisterFFT(float[], int, float[]) - Constructor for class registration.RegisterFFT
Prepare for registration including preprocessing of the reference image.
RegisterFFTHessian - class registration.RegisterFFTHessian.
Registration using Hessian eigenvalues edge detection and Fourier transform cross-correlation.
RegisterFFTHessian(float[], int) - Constructor for class registration.RegisterFFTHessian
Prepare for registration including preprocessing of the reference image.
RegisterFFTHessian(float[], int, float[]) - Constructor for class registration.RegisterFFTHessian
Prepare for registration including preprocessing of the reference image.
registerFrames(float[][], int, int, int, String) - Method in class retina.ScriptProcessor
Register frames in a to the first frame in a.
RegisterMI - class registration.RegisterMI.
Registration using mutual information.
RegisterMI() - Constructor for class registration.RegisterMI
Zero instantiation
RegisterMI(float[], int) - Constructor for class registration.RegisterMI
Prepare for registration including preprocessing of the reference image.
RegisterRetina - class registration.RegisterRetina.
Retina registration methods.
RegisterRetina(float[], int, float[]) - Constructor for class registration.RegisterRetina
Prepare for registration including preprocessing of the reference image.
registration - package registration
 
REGISTRATIONOFFSET - Static variable in class retina.RetinalImage
On the last line, from the left edge this space is used as registration parameters.
reinit(int) - Method in class numericalMethods.calculus.odeSolving.BulirschStoer.TempDataContainer
 
relTol - Variable in class numericalMethods.calculus.integration.ExtrapIntegrator
 
remove(int) - Method in class net.sourceforge.jannealer.SimplexList
Removes a Simplex from the SimplexList
removeExtension(String) - Static method in class retina.ScriptProcessor
 
removePropertyChangeListener(PropertyChangeListener) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
removePropertyChangeListener(PropertyChangeListener) - Method in class numericalMethods.calculus.odeSolving.RungeKutta
 
removePropertyChangeListener(PropertyChangeListener) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
removePropertyChangeListener(PropertyChangeListener) - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
removePropertyChangeListener(PropertyChangeListener) - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
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
replaceNeighbor(int, int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
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.
residuals(float[], float[]) - Static method in class bijnum.BIJstats
Compute residuals of b versus a.
resize(double[], int) - Static method in class numericalMethods.util.Arrays
Like Arrays.size(double[],int) but copies also the contents of the target if nessecary.
resize(double[], int, int) - Static method in class numericalMethods.util.TupleSequences
Like newSize but copies also the contents of the target if nesescary.
resize(float[], int) - Static method in class numericalMethods.util.Arrays
Like Arrays.size(float[],int) but copies also the contents of the target if nessecary.
resize(int[], int) - Static method in class numericalMethods.util.Arrays
Like Arrays.size(int[],int) but copies also the contents of the target if nessecary.
result - Variable in class volume.Diffusion
 
result() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
retina - package retina
 
RetinalImage - class retina.RetinalImage.
This class contains methods to process retinal images.
RetinalImage() - Constructor for class retina.RetinalImage
 
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
 
rightEye - Variable in class retina.OIDHeader
 
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.
round(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Rounds matrix A and stores result in B.
round(double[][], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Rounds matrix A and stores result in B.
round(double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Rounds vector a and stores result in b .
round(double[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Rounds vector a and stores result in b .
rp - Static variable in class FlowJ.FlowJSpotNoise
 
rs - Variable in class VolumeJ.VJUserInterface
 
RTA_Reader - class retina.RTA_Reader.
This class implements a Talia Inc Retinal Thickness (www.talia.com) Analyzer thickness map format (.m) file reader.
RTA_Reader() - Constructor for class retina.RTA_Reader
 
RTA_Thickness_Reader - class retina.RTA_Thickness_Reader.
This class implements a Talia Inc Retinal Thickness (www.talia.com) Analyzer thickness map format (.m) file reader.
RTA_Thickness_Reader() - Constructor for class retina.RTA_Thickness_Reader
 
RTAReader - class retina.RTAReader.
This class implements a Talia Inc Retinal Thickness (www.talia.com) Analyzer thickness map format (.m) file reader.
RTAReader() - Constructor for class retina.RTAReader
 
RUN - Static variable in class retina.ScriptProcessor
 
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() - Method in class retina.OIDStackWindow
 
run() - Method in class retina.OIDWindow
 
run() - Method in class va.VideoWatch
Updates the video frame ImagePlus to show the current video frame.
run() - Method in class va.TimedAcquisition
Grabs a frame at the required frame rate.
run() - Method in class va.VideoAcq
Updates the video frame ImagePlus to show the current video frame.
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
 
run(String) - Method in class retina.RTA_Thickness_Reader
 
run(String) - Method in class retina.RTA_Reader
 
RungeKutta - class numericalMethods.calculus.odeSolving.RungeKutta.
 
RungeKutta() - Constructor for class numericalMethods.calculus.odeSolving.RungeKutta
 
rungeKutta(DoubleArrayParametrized, DoubleArrayValued, double[], double, double) - Static method in class numericalMethods.calculus.odeSolving.RungeKutta
 
rungeKutta(DoubleArrayParametrized, DoubleArrayValued, double[], double, double, double[], double[], double[], double[], double[]) - Static method in class numericalMethods.calculus.odeSolving.RungeKutta
 
RungeKutta(int) - Constructor for class numericalMethods.calculus.odeSolving.RungeKutta
 
RungeKuttaFehlberg - class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg.
 
RungeKuttaFehlberg() - Constructor for class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
RungeKuttaFehlberg(int) - Constructor for class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
RungeKuttaFehlbergIntegrator - class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator.
 
RungeKuttaFehlbergIntegrator() - Constructor for class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
RungeKuttaFehlbergIntegrator(DoubleParametrized, DoubleArrayValued) - Constructor for class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
RungeKuttaFehlbergIntegrator(DoubleParametrized, DoubleArrayValued, boolean) - Constructor for class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
RungeKuttaFehlbergIntegrator(int) - Constructor for class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
RungeKuttaFehlbergIntegrator(int, boolean) - Constructor for class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
rungeKuttaStep(DoubleArrayParametrized, DoubleArrayValued, double[], double, double[], double[], double[], double[], double[]) - Static method in class numericalMethods.calculus.odeSolving.RungeKutta
 
running - Variable in class VolumeJ.VJRenderView
 
running - Variable in class VolumeJ.VJRenderer
Flag indicating whether this renderer is running.
running - Variable in class va.VideoWatch
 
running - Variable in class va.TimedAcquisition
 
running - Variable in class va.VideoAcq
 
runs(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns the runs of a given permutation, as int arrays.
Ruppert - class numericalMethods.geometry.meshGeneration.ruppert.Ruppert.
 
Ruppert(double[][]) - Constructor for class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
RXB - class numericalMethods.algebra.linear.solve.RXB.
Computes for a system of equations R·X=B with given right triangular matrix R and matrix B the solving matrix X.
RXB() - Constructor for class numericalMethods.algebra.linear.solve.RXB
 

S

s - Variable in class VolumeJ.VJCell
 
s - Variable in class VolumeJ.VJBinaryShell
 
S - Variable in class bijnum.BIJfht
 
S - Variable in class bijnum.BIJfft
 
S(float[], float[], int, double, double, double, String) - Static method in class knn.StereoFilterBank
Compute a stereo difference image.
SAFE1 - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
SAFE2 - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
SAFETY - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
SAFETY - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
salgorithm - Static variable in class bd.BlobDetector
 
sample(int[]) - Method in class knn.Features
Return a new Features with all Feature element arrays containing only the elements in indices.
sampleEvenImages(float[][]) - Static method in class stereodisk.StereoDiskAnalyzer
Subsample the even images from images and convert to a vector array (which is much smaller).
sampleFeatureImagePixels(String, String[], boolean) - Static method in class stereodisk.StereoDiskAnalyzer
Obtain half of all images for all features in names, and compact into a MxN vector, where N is the number of features and M is the number of subsampled pixels in all images.
sampleFeatureImagePixels(String, String, boolean) - Static method in class stereodisk.StereoDiskAnalyzer
Obtain half of all images for the feature in name, and compact into a Mx1 vector, where M is the number of subsampled pixels in all images.
sampleGroundTruthTestingPixels(float[][]) - Static method in class stereodisk.StereoDiskANNTester
 
sampleGroundTruthTestingPixels(float[][]) - Static method in class stereodisk.StereoDiskROC
 
sampleGroundTruthTrainingPixels(float[][]) - Static method in class stereodisk.StereoDiskANNTester
 
sampleGroundTruthTrainingPixels(float[][]) - Static method in class stereodisk.StereoDiskROC
 
sampleImages(float[][], boolean) - Static method in class stereodisk.StereoDiskAnalyzer
Sample the images either odd or even from images and convert to a vector array (which is much half the size).
sampleOddImages(float[][]) - Static method in class stereodisk.StereoDiskAnalyzer
Sample the odd images from images and convert to a vector array (which is much smaller).
save(float[][], int, String, String) - Static method in class retina.OIDPCAAnalyzer
Dump the matrix m as a raw float stack to disk.
saveAnalysis(float[][], float[][], int, String, boolean) - Method in class retina.OIDAnalyzer
 
saveAnalysis(float[][], int, String, String, boolean) - Method in class retina.ScriptProcessor
Save the analysis in images.
saveAsciiImage(ImagePlus, String, String) - Static method in class stereodisk.StereoDiskPGMConverter
 
saveAsObject(String) - Method in class of3d.OF3DFlow
 
saveAsTable(float[][], float[][], float[], String, String) - Method in class retina.ScriptProcessor
Save the vectors avg, below, above, and x as an Excel compatible, tab separated table.
saveAsTable(float[], float[], float[], String, String) - Method in class retina.ScriptProcessor
Save the vectors avg, below, above, and x as an Excel compatible, tab separated table.
saveAsTable(float[], String, String) - Method in class retina.ScriptProcessor
Save the vectors avg, and x as an Excel compatible, tab separated table.
saveAsTable(StringBuffer, String, String) - Method in class retina.ScriptProcessor
Save the vectors avg, below, above, and x as an Excel compatible, tab separated table.
saveAsTable(String, float[][][], float[][][], float[], float[]) - Static method in class retina.OIDroiTCAnalyzer
Save the 3-d matrices avg and sem in the following Excel compatible format.
saveAsText(float[], String) - Static method in class bijnum.BIJutil
Save vector v as a text file.
saveFrames(float[][], int, String, String) - Static method in class retina.ScriptProcessor
Save the aggregated frames.
saveRegistrationAsTable(float[], float[], float[], String) - Method in class retina.ScriptProcessor
Save the vectors with the x, y and rotation registration parameters into a Excel readblae separated file.
saveTimecourse(int, int, int) - Method in class retina.OIDStackWindow
Save the timecourse as a TIFF file.
saveTimecourse(String, String, float[][], int, int, int) - Static method in class retina.OIDAnalysis
Save the timecourse for a as a TIFF file.
scale - Variable in class VolumeJ.VJRenderView
State variables.
scale - Static variable in class VolumeJ.VJUserInterface
 
scale - Variable in class bijnum.BIJmi
 
scale - Static variable in class retina.OIDReconstructor
 
scale - Variable in class retina.OIDProcessor
 
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
 
scaleField - Variable in class bd.BDUserInterface
 
scales - Variable in class knn.FilterBank
 
scales - Variable in class knn.StereoFilterBank
 
scales - Static variable in class knn.FeatureComputer
 
scaleSet(int) - Static method in class knn.FilterBank
Return a set of n good scales for scale space.
scaleSpaceContrast - Variable in class volume.Diffusion
 
scaleSpaceContrast - Variable in class volume.Diffusion3D
 
scaling - Static variable in class retina.OIDReconstructor
 
scaling - Variable in class retina.OIDProcessor
 
scaling - Static variable in class stereodisk.StereoDiskFeatureConverter
 
SCALMX - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
Schedule - class net.sourceforge.jannealer.Schedule.
This class contains the Annealing scheme.
Schedule(AnnealingScheme) - Constructor for class net.sourceforge.jannealer.Schedule
Constructor for the Schedule object
scriptFilePath - Variable in class retina.ScriptProcessor
The name of the file that controls this OIDFileProcessor.
scriptProcessor - Static variable in class retina.OIDAnalyzer
 
scriptProcessor - Static variable in class retina.OIDMapsFitter
 
scriptProcessor - Static variable in class retina.OIDroiAnalyzer
 
scriptProcessor - Static variable in class retina.OIDPCAAnalyzer
 
scriptProcessor - Static variable in class retina.OIDROItimecourseAnalyzer
 
ScriptProcessor - class retina.ScriptProcessor.
Class to process / analyze OID files and directories of OID using a script file.
ScriptProcessor(String, String) - Constructor for class retina.ScriptProcessor
Create a new OIDFileProcessor to process the control file.
ScriptProcessor(String, String, boolean) - Constructor for class retina.ScriptProcessor
Create a new OIDFileProcessor to process the control file.
ScriptProcessor(String, String, OIDBaseAnalyzer) - Constructor for class retina.ScriptProcessor
Create a new OIDFileProcessor that can call back to an analyzer.
sderiv - Static variable in class FlowJ.FlowJLucas
 
sderiv - Static variable in class bd.BlobDetector
 
sderiv - Static variable in class of3d.OF3DLucas
 
search() - Method in class numericalMethods.calculus.minimizing.LineNDDBrent
 
search() - Method in class numericalMethods.calculus.minimizing.nmLineNDBrent
 
search(double[], double[][], double, nmDoubleArrayParametrized, nmDoubleValued) - Static method in class numericalMethods.calculus.minimizing.nmPowell
 
search(double[], double[][], double, nmDoubleArrayParametrized, nmDoubleValued, int, boolean) - Static method in class numericalMethods.calculus.minimizing.nmPowell
 
search(double[], double[][], double, nmDoubleValued) - Static method in class numericalMethods.calculus.minimizing.nmPowell
 
search(double[], double[], DoubleParametrized, DoubleValued, DoubleValued, double) - Static method in class numericalMethods.calculus.minimizing.DBrent
 
search(double[], double[], nmDoubleValued) - Static method in class numericalMethods.calculus.minimizing.nmBracket
 
search(double[], double[], nmDoubleValued, double) - Static method in class numericalMethods.calculus.minimizing.nmBrent
 
search(double[], double, DoubleArrayParametrized, DoubleValued, DoubleArrayValued) - Static method in class numericalMethods.calculus.minimizing.ConjugateGradient
 
search(double[], double, DoubleArrayParametrized, DoubleValued, DoubleArrayValued, int, boolean, boolean) - Static method in class numericalMethods.calculus.minimizing.ConjugateGradient
 
search(double[], double, DoubleValued) - Static method in class numericalMethods.calculus.minimizing.ConjugateGradient
 
search(double[], double, nmDoubleArrayParametrized, nmDoubleValued, int, boolean) - Static method in class numericalMethods.calculus.minimizing.nmPowell
 
search(double[], double, nmDoubleValued) - Static method in class numericalMethods.calculus.minimizing.nmPowell
 
search(DoubleArrayParametrized, DoubleArrayValued, double, double, double[]) - Static method in class numericalMethods.calculus.rootFinding.NewtonRaphson
Performs Newton´s method starting at z=x+iy.
search(DoubleArrayParametrized, DoubleArrayValued, double, double, double[], double) - Static method in class numericalMethods.calculus.rootFinding.NewtonRaphson
Performs Newton´s method starting at z=x+iy.
search(DoubleArrayParametrized, DoubleArrayValued, double, double, double[], double, double, double, double, double, double, double, int, boolean) - Static method in class numericalMethods.calculus.rootFinding.NewtonRaphson
Performs Newton´s method starting at z=x+iy and restricting itself to the rectangle [xMin,xMax]x[yMin,yMax].
search(double, double, double, double[], DoubleParametrized, DoubleValued, DoubleValued, double) - Static method in class numericalMethods.calculus.minimizing.DBrent
 
search(double, double, double, double[], DoubleValued, double) - Static method in class numericalMethods.calculus.minimizing.Golden
 
search(double, double, double, double[], nmDoubleValued, double) - Static method in class numericalMethods.calculus.minimizing.nmBrent
 
search(DoubleParametrized, DoubleArrayValued, double, double[]) - Static method in class numericalMethods.calculus.rootFinding.NewtonRaphson
Performs Newton´s method starting at x.
search(DoubleParametrized, DoubleArrayValued, double, double[], double) - Static method in class numericalMethods.calculus.rootFinding.NewtonRaphson
Performs Newton´s method starting at x.
search(DoubleParametrized, DoubleArrayValued, double, double[], double, double, double, double, int, boolean) - Static method in class numericalMethods.calculus.rootFinding.NewtonRaphson
Performs Newton´s method starting at x and restricting itself to the interval [xMin,xMax].
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.
SearchMI - class registration.SearchMI.
This class extends BIJmi to provide hooks for the numericalMethods minimization routines package.
SearchMI(float, float, float, float[], float[], int) - Constructor for class registration.SearchMI
Create a new MI search object for images a and b.
SECOND - Static variable in class numericalMethods.algebra.loopGroup.BirkhoffFactorization
 
secondaryClassifier - Variable in class VolumeJ.VJClassifier
Contains a secondary classifier if needed in alphacolor.
seekAndMarkSegment(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
seekSegment(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
segment - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
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[]) - 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.
separate - Variable in class bd.BDUserInterface
 
SEPARATE - Static variable in class retina.OIDProcessor
 
SEPARATE - Static variable in class retina.OIDAnalysis
 
sequenceNumber - Variable in class VolumeJ.VJRenderer
 
set(double, double) - Method in class numericalMethods.function.util.AbstractValueCacher.Key
 
set(double, double[], int) - Method in class numericalMethods.function.util.AbstractValueCacher.Key
 
set(int, double) - Method in class retina.ScriptProcessor
Set parameter ix to value value.
set(int, int, double) - Method in class Jama.Matrix
Set a single element.
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.
setAbsTol(double) - Method in class numericalMethods.calculus.integration.ExtrapIntegrator
 
setAbsTol(double) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
setAlpha(float) - Method in class VolumeJ.VJAlphaColor
 
setAnalyzer(OIDBaseAnalyzer) - Method in class retina.ScriptProcessor
 
setAngleConstraint(double) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
setAreaConstraint(double) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
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.
setByParameter(double[]) - Method in class numericalMethods.calculus.minimizing.NumericalGradient
 
setByParameter(double[]) - Method in class numericalMethods.calculus.minimizing.Quadric
 
setByParameter(double[]) - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.ComplexSinus
 
setCachValues(boolean) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
setCalibration(Calibration) - Method in class FlowJ.FlowJFlow
 
setClassifier(VJClassifier) - Method in class VolumeJ.VJRenderer
 
setCoolingRate(double) - Method in class net.sourceforge.jannealer.AnnealingScheme
Sets the CoolingRate attribute of the AnnealingScheme object
setCurrentStepSize(double) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
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
setDebug(boolean) - Static method in class numericalMethods.calculus.minimizing.nmPowell
Set the value of debug.
setDebug(boolean) - Static method in class numericalMethods.calculus.minimizing.ConjugateGradient
Set the value of debug.
setDebug(boolean) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
setDescription(String) - Method in class VolumeJ.VJRenderer
 
setDirection(double[]) - Method in class numericalMethods.calculus.minimizing.nmLineND
Set the value of direction.
setDisplayed(Object) - Method in class FlowJ.FlowJCanvas
 
setDoubleArrayParameter(double[], int) - Method in class numericalMethods.calculus.minimizing.NumericalGradient
 
setDoubleArrayParameter(double[], int) - Method in class numericalMethods.calculus.minimizing.Quadric
 
setDoubleArrayParameter(double[], int) - Method in class numericalMethods.calculus.odeSolving.ExampleODE.F
Evaluates the derivatives
setDoubleArrayParameter(double[], int) - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.ComplexSinus
 
setDoubleArrayParameter(double[], int) - Method in interface numericalMethods.function.nmDoubleArrayParametrized
Set the double array parameter by the values in a double[].
setDoubleArrayParameter(double[], int) - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
setDoubleArrayParameter(double[], int) - Method in class registration.SearchMI
Required because implements nmDoubleArrayParametrized.
setDoubleArrayValueLength(int) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
setDoubleArrayValueLength(int) - Method in interface numericalMethods.calculus.integration.DoubleArrayValuedIntegrator
 
setDoubleArrayValueLength(int) - Method in class numericalMethods.function.util.AbstractValueCacher
 
setDoubleArrayValueLength(int) - Method in class numericalMethods.function.util.DoubleArrayValueCacher
 
setDoubleParameter(double) - Method in class numericalMethods.calculus.integration.ExampleIntegration.F
Evaluates the derivatives
setDoubleParameter(double) - Method in class numericalMethods.calculus.minimizing.nmLineND
 
setDoubleParameter(double) - Method in class numericalMethods.calculus.minimizing.nmLineNDEvaluator
 
setDoubleParameter(double) - Method in class numericalMethods.calculus.minimizing.LineNDDBrent.projectedGradient
 
setDoubleParameter(double) - Method in class numericalMethods.calculus.minimizing.Sin
 
setDoubleParameter(double) - Method in class numericalMethods.calculus.minimizing.Cos
 
setDoubleParameter(double) - Method in class numericalMethods.calculus.rootFinding.ExampleNewtonRaphson.RealSinus
 
setDoubleParameter(double) - Method in interface numericalMethods.function.nmDoubleParametrized
Set the double parameter.
setDoubleParameter(double) - Method in class numericalMethods.function.util.AbstractValueCacher
 
setDoubleParameter(int, double) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
setEdge(int) - Method in class volume.Volume
Set the edges in the volume beyond which a voxel is not valid.
setEps(double) - Method in class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
setEps(double) - Method in class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
setEps(double) - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
setEps(double) - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
setEps(double) - Method in class numericalMethods.function.util.AbstractValueCacher
 
setExtraInfo(String) - Method in class retina.OIDHeader
 
setFields(Label, Label, Label, Label) - Method in class FlowJ.FlowJCanvas
 
setFloatArrayParameter(float[], int) - Method in interface numericalMethods.function.FloatArrayParametrized
Set the float array parameter by the values in a float[].
setFloatParameter(float) - Method in interface numericalMethods.function.FloatParametrized
Set the float parameter.
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.
setFunction(DoubleParametrized, DoubleArrayValued) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
setFunction(DoubleParametrized, DoubleArrayValued) - Method in interface numericalMethods.calculus.integration.DoubleArrayValuedIntegrator
 
setFunction(DoubleParametrized, DoubleArrayValued) - Method in class numericalMethods.function.util.DoubleArrayValueCacher
 
setFunction(DoubleParametrized, DoubleValued) - Method in class numericalMethods.function.util.DoubleValueCacher
 
setFunction(ObjectiveFunction) - Method in class net.sourceforge.jannealer.AnnealingScheme
 
setH(double) - Method in class numericalMethods.calculus.minimizing.NumericalGradient
Set the value of h.
setHeader(byte[]) - Method in class retina.OIDHeader
 
setHeader(OIDHeader) - Method in class retina.OIDProcessor
Set the OID header obtained from OID info.
setHeight(int) - Method in class retina.OIDHeader
 
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
 
setInitialStepSize(double) - Method in class numericalMethods.calculus.integration.ExtrapIntegrator
 
setInitialStepSize(double) - Method in class numericalMethods.calculus.integration.BulirschStoerIntegrator
 
setInitialStepSize(double) - Method in class numericalMethods.calculus.integration.RungeKuttaFehlbergIntegrator
 
setIntegerArrayParameter(int[], int) - Method in interface numericalMethods.function.IntegerArrayParametrized
Set the integer array parameter by the values in an int[].
setIntegerParameter(int) - Method in interface numericalMethods.function.IntegerParametrized
Set the integer parameter.
setInterpolator(VJInterpolator) - Method in class VolumeJ.VJRenderer
 
setIntParameter(int, int) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
setIter(int) - Method in class net.sourceforge.jannealer.Schedule
Sets the Iter attribute of the Schedule object
setIterations(int) - Method in class net.sourceforge.jannealer.AnnealingScheme
Number of iterations before cooling is applied
setITMAX(double) - Static method in class numericalMethods.calculus.minimizing.nmBrent
Set the value of ITMAX.
setITMAX(int) - Static method in class numericalMethods.calculus.minimizing.DBrent
Set the value of ITMAX.
setITMAX(int) - Static method in class numericalMethods.calculus.minimizing.nmPowell
Set the value of ITMAX.
setITMAX(int) - Static method in class numericalMethods.calculus.minimizing.ConjugateGradient
Set the value of ITMAX.
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.
setMatrix(int[], int[], Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int[], int, int, Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int, int, int[], Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int, int, int, int, Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMax(int, double) - Method in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
setMaximalNumberOfTriangles(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
setMaxTableSize(int) - Method in class numericalMethods.calculus.odeSolving.Extrap
sets the maximal number of columns in interpolation table.
setMessage(String) - Method in class VolumeJ.VJRenderer
Set the rendering message.
setMin(int, double) - Method in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
setN(int) - Method in class numericalMethods.calculus.minimizing.nmLineND
Set the value of n.
setNumOfEquations(int) - Method in class numericalMethods.calculus.odeSolving.RungeKutta
 
setNumOfEquations(int) - Method in interface numericalMethods.calculus.odeSolving.OdeSolver
 
setNumOfEquations(int) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
setNumOfEquations(int) - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
setNumOfEquations(int) - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
setOffsetFromSimplex(double[]) - Method in class net.sourceforge.jannealer.AnnealingScheme
 
setOpaque() - Method in class VolumeJ.VJAlphaColor
 
setOptions(boolean, boolean, boolean, boolean, boolean, float, float, int, int, int, int) - Method in class retina.OIDProcessor
Set the options for this OIDProcessor.
setOutputColor() - Method in class VolumeJ.VJRenderer
Set the output to color.
setOutputGrayscale() - Method in class VolumeJ.VJRenderer
Set the output to color.
setPDiagonal() - Method in class net.sourceforge.jannealer.Schedule
Sets the PDiagonal attribute of the Schedule object
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.
setPoint(double[]) - Method in class numericalMethods.calculus.minimizing.nmLineND
Set the value of point.
setProcessing(String) - Method in class retina.OIDHeader
Prepend a modification String to the headerinfo so we know it is the result of processing.
setProcessor(ImagePlus) - Method in class va.VideoWatch
 
setProcessor(ImagePlus) - Method in class va.VideoAcq
 
setProperties(int, int, int, String) - Method in class retina.OIDHeader
 
setPsum(int) - Method in class net.sourceforge.jannealer.Schedule
Sets the Psum attribute of the Schedule object
setRadius(double) - Method in class registration.LocatedCircle
 
setRegistration(boolean) - Method in class retina.ScriptProcessor
Set extra registration flag on or off.
setRegistrationParameters(float[], int, float[]) - Static method in class retina.RetinalImage
Store the registration parameters (max REGISTRATIONOFFSET) into the bottom left pixels of the image Parameters start from the left with parameters[0], 1 pixel for parameters[2] etc.
setRelTol(double) - Method in class numericalMethods.calculus.integration.ExtrapIntegrator
 
setRelTol(double) - Method in class numericalMethods.calculus.odeSolving.Extrap
 
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.
setSolution(double[]) - Method in class net.sourceforge.jannealer.AnnealingScheme
Sets a starting point for searching for a solution
setStackSize(int) - Method in class retina.OIDHeader
 
setStaticVolume(Volume) - Method in class of3d.OF3DFlow
Sets a secondary static volume for which the flow has been computed.
setStepSize(double) - Method in class numericalMethods.calculus.odeSolving.RungeKutta
 
setStepSize(double) - Method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
setStepSize(double) - Method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
setStimulus(String) - Method in class retina.OIDHeader
 
setStimulusEndFrame(int) - Method in class retina.OIDHeader
 
setStimulusParameter(float[], int, int) - Static method in class retina.RetinalImage
Store the stimulus flag into the bottom left pixels of the image
setStimulusStartFrame(int) - Method in class retina.OIDHeader
 
setT(double) - Method in class numericalMethods.calculus.minimizing.nmLineND
Set the value of t.
setTemperature(double) - Method in class net.sourceforge.jannealer.AnnealingScheme
Sets the Temperature attribute of the AnnealingScheme object
setThreshold(double) - Method in class bd.BlobDetector
 
setThreshold(float) - Method in class VolumeJ.VJClassifierIsosurface
 
setThreshold(float) - Method in class VolumeJ.VJClassifierLevoy
Set center of gradient tent function.
setTolerance(double) - Method in class net.sourceforge.jannealer.AnnealingScheme
Sets the Tolerance attribute of the AnnealingScheme object.
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.
setTriangle(Ruppert) - Method in class numericalMethods.geometry.meshGeneration.ruppert.DelaunayViewer
 
setup() - Method in class bd.BDColorSeparator
 
setup() - Method in class of3d.OFClassifierScintillans
 
setup(double) - Method in class bd.BDVarDetector
 
setup(double, int, int) - Method in class bd.BlobDetector
 
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.
setUseDBrent(boolean) - Static method in class numericalMethods.calculus.minimizing.ConjugateGradient
Set the value of useDBrent.
setVerbosity(int) - Method in class retina.ScriptProcessor
 
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.
setWidth(int) - Method in class retina.OIDHeader
 
setx(int) - Method in class VolumeJ.VJVoxelLoc
Set the value for x.
setY(double[]) - Method in class net.sourceforge.jannealer.Schedule
Sets the Y attribute of the Schedule object
sety(int) - Method in class VolumeJ.VJVoxelLoc
Set the value for x.
setYb(double) - Method in class net.sourceforge.jannealer.Schedule
Sets the Yb attribute of the Schedule object
setz(float) - Method in class VolumeJ.VJVoxelLoc
Set the value for z.
setz(int) - Method in class VolumeJ.VJVoxelLoc
Set the value for z.
setZero(int, double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
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.
shift_scales - Static variable in class knn.FeatureComputer
 
shiftPoints() - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
shortMatrixFromImageStack(ImagePlus) - Static method in class bijnum.BIJutil
Convert the data in the ImageStack in imp into a short [][] matrix for further processing.
show - Variable in class va.VideoWatch
 
show() - Method in class FlowJ.FlowJUserInterface
Shows Dialog.
show() - Method in class bd.BDUserInterface
 
show(double[][], String) - Static method in class numericalMethods.algebra.linear.decompose.TestTridiagonal
 
show(double[][], String) - Static method in class numericalMethods.algebra.linear.decompose.TestCholesky
 
showAccuracies(Features, float[], Features, float[], int, int) - Static method in class stereodisk.StereoDiskAnalyzer
Print the accuracies for each feature used in knn search.
showAndSavePlot(float[], float[], float[], String, String, String) - Method in class retina.ScriptProcessor
 
showAndSavePlots(float[][], float[][], float[], String, String, String, float[][], int) - Method in class retina.ScriptProcessor
Show and save plots of timecourses in tc.
showAndSaveResults(double[][], double[][], int, String, String) - Static method in class retina.OIDroiAnalyzer
Plot the averages in the column vectors of avg, and also plot CI for avg.
showAndSaveResults(String, double[][][], double[][][], String, String) - Static method in class retina.OIDroiTCAnalyzer
Plot all signals for each condition and ROI, with their CI.
showAndSaveResults(String, float[][], int, String, String) - Static method in class retina.OIDamplitudeAnalyzer
Plot all signals for each condition and ROI, with their CI.
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
 
showDialog() - Method in class retina.RTA_Thickness_Reader
 
showDialog() - Method in class retina.RTA_Reader
 
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
 
showFileHeader(File) - Method in class retina.OIDReconstructor
A file has been selected.
showFiles(List, String, Object) - Method in class io.OpenPreviewDialog
Fill the list with all files from the directory that fit filter.
showGUI() - Method in class va.VAInterface
Sets up the dialog window with all (dynamic) elements filled in.
showProgress(float) - Static method in class FlowJ.FlowJUserInterface
 
showResume() - Method in class va.VideoWatch
 
showStatisticsPerClass(String[], float[][][], float[][], int, String) - Static method in class stereodisk.StereoDiskGroundTruthAnalyzer
Show the statistics for the class c and ground truths gt.
showStatus(String) - Static method in class FlowJ.FlowJUserInterface
 
showVectorAsImage(float[], int) - Static method in class bijnum.BIJutil
 
showWait() - Method in class va.VideoWatch
 
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
 
SIGMA_RELATIVE - Static variable in class volume.DoG2D
 
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.
Simplex - class net.sourceforge.jannealer.Simplex.
Holds the vertices of the simplex and the function value at the vertices
simplex() - Method in class net.sourceforge.jannealer.AnnealingScheme
finds a solution using downhill simplex.
Simplex(double[], double, int) - Constructor for class net.sourceforge.jannealer.Simplex
Constructor for the Simplex object
SimplexList - class net.sourceforge.jannealer.SimplexList.
An ArrayList of Simplex Objects
SimplexList(int) - Constructor for class net.sourceforge.jannealer.SimplexList
Constructor for the SimplexList object
simpsonSum(double[]) - Static method in class numericalMethods.calculus.integration.NewtonCotes
 
Sin - class numericalMethods.calculus.minimizing.Sin.
 
Sin() - Constructor for class numericalMethods.calculus.minimizing.Sin
 
singlechannel() - Method in class VolumeJ.VJShade
 
SingularValueDecomposition - class Jama.SingularValueDecomposition.
Singular Value Decomposition.
SingularValueDecomposition(Matrix) - Constructor for class Jama.SingularValueDecomposition
Construct the singular value decomposition
size - Variable in class retina.OIDamplitudeAnalyzer
 
size() - Method in class net.sourceforge.jannealer.SimplexList
Returns the size of the ArrayList
size(double[], int) - Static method in class numericalMethods.util.Arrays
Just returns target if its length equals size.
size(double[], int, int) - Static method in class numericalMethods.util.TupleSequences
Just returns target if its length equals tupleSize times size.
size(float[], int) - Static method in class numericalMethods.util.Arrays
Just returns target if its length equals size.
size(int[], int) - Static method in class numericalMethods.util.Arrays
Just returns target if its length equals size.
sKernel - Variable in class FlowJ.FlowJLucas
 
SKIPODDS - Static variable in class retina.ScriptProcessor
 
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.
SLIDINGWINDOWSIZE - Static variable in class retina.RetinalImage
Size of sliding window in pixels for equalization and vignetting removal.
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.
solve(double[][], double[]) - Static method in class numericalMethods.algebra.linear.solve.RXB
Solves a system of real equations.
solve(double[][], double[]) - Static method in class numericalMethods.algebra.linear.solve.LXB
Solves a system of real equations.
solve(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.solve.RXB
Solves a system of real equations.
solve(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.solve.LXB
Solves a system of real equations.
solve(double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.solve.RXB
Solves a system of real equations.
solve(double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.solve.LXB
Solves a system of real equations.
solve(double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.solve.AXB
Minimizes a system of real valued equations.
solve(double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.solve.RXB
Solves a system of complex equations.
solve(double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.solve.LXB
Solves a system of complex equations.
solve(double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.solve.RXB
Solves a system of complex equations.
solve(double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.solve.LXB
Solves a system of complex equations.
solve(double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.solve.AXB
Minimizes a system of complex valued equations.
solve(double[][], double[][], double[][], double[][], double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.AXB
Minimizes a system of complex valued equations.
solve(double[][], double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.RXB
Solves a system of complex equations.
solve(double[][], double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.LXB
Solves a system of complex equations.
solve(double[][], double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.AXB
Minimizes a system of real valued equations.
solve(double[][], double[][], double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.RXB
Solves a system of complex equations.
solve(double[][], double[][], double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.LXB
Solves a system of complex equations.
solve(double[][], double[][], double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.AXB
Minimizes a system of complex valued equations.
solve(double[][], double[][], double[], double[], double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.AXB
Minimizes a system of complex valued equations.
solve(double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.RXB
Solves a system of real equations.
solve(double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.LXB
Solves a system of real equations.
solve(double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.AXB
Minimizes a system of real valued equations.
solve(double[][], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.solve.AXB
Minimizes a system of real valued equations.
solve(Matrix) - Method in class Jama.Matrix
Solve A*X = B
solve(Matrix) - Method in class Jama.LUDecomposition
Solve A*X = B
solve(Matrix) - Method in class Jama.QRDecomposition
Least squares solution of A*X = B
solve(Matrix) - Method in class Jama.CholeskyDecomposition
Solve A*X = B
solveTranspose(Matrix) - Method in class Jama.Matrix
Solve X*A = B, which is also A'*X' = B'
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.
sortByCondition(String, String[], boolean) - Method in class retina.OIDReconstructor
Sort the selected epochs (from a single experiment) epochNames on stimulus condition and save the frames as a single file in the same format.
sortNamesByCondition(String, String[]) - Method in class retina.OIDReconstructor
Sort the names of the selected epochs (from a single experiment) on stimulus condition.
sourceChoice - Variable in class VolumeJ.VJUserInterface
 
spawnWaveform(float[], int, int, int, int) - Static method in class retina.OIDAnalysis
Waveform describes the form of the signal for a single condition, and should be 0 where the truncation should be indifferent.
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[]) - 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.
spectralAnalysis(float[][][], int, double, String) - Static method in class retina.OIDAnalysis
Spectral analysis of timecourse data, Data is organized as r[j][k][i] where j is the condition, k is the frame number relative to the start of the cycle, and i is the repeat number.
spectrum(float[]) - Static method in class bijnum.BIJstats
Compute the spectrum of v.
specular - Variable in class VolumeJ.VJLight
 
splitEdge(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
splitEdge(int, int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
splitTriangle(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
splitTriangle(int) - Method in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
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
 
spread() - Method in class net.sourceforge.jannealer.SimplexList
Computes the difference between the maximum and the minimum values of the elements of the SimplexList, excluding the last Simplex added
sqr(double) - Static method in class numericalMethods.calculus.minimizing.nmPowell
 
sqrLeastDistance - Variable in class numericalMethods.geometry.meshGeneration.ruppert.Ruppert
 
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
 
start - Static variable in class retina.OIDReconstructor
 
start - Variable in class retina.OIDProcessor
Other parameters describing the layout of aggregate.
start - Variable in class va.TimedAcquisition
 
START - Static variable in class retina.ScriptProcessor
 
startAt(double) - Method in class numericalMethods.calculus.integration.OdeSolverBasedIntegrator
 
startAt(double) - Method in class numericalMethods.calculus.integration.ExtrapIntegrator
 
startAt(double) - Method in interface numericalMethods.calculus.integration.DoubleArrayValuedIntegrator
 
startdir - Static variable in class retina.OIDReconstructor
 
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
 
stateKey - Variable in class numericalMethods.function.util.AbstractValueCacher
 
stateT - Variable in class numericalMethods.function.util.AbstractValueCacher
 
staticPixel - Variable in class of3d.OFClassifierScintillans
 
stats(double[][], double[][], float[][], int, int, int, int, int, int) - Static method in class retina.OIDroiAnalyzer
Compute signal and SEM for all ROIs for the frame of condition j, frame k.
statsROIBaselineCondition(double[][][], double[][][], float[][], int, int, int, int, int, int, int) - Static method in class retina.OIDroiTCAnalyzer
Compute signal and SEM for all ROIs for the frame of condition j, frame k.
statsROIPrestimulusAverage(double[][][], double[][][], float[][], int, int, int, int, int, float[]) - Static method in class retina.OIDroiTCAnalyzer
Compute signal and SEM for all ROIs for the frame of condition j, frame k.
statsROISameImage(double[][][], double[][][], float[][], int, int, int, int, int, boolean) - Static method in class retina.OIDroiTCAnalyzer
Compute signal and SEM for all ROIs for the frame of condition j, frame k.
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.
step(DoubleArrayParametrized, DoubleArrayValued, double[], double[], double[], double[], double[], BulirschStoer.TempDataContainer) - Static method in class numericalMethods.calculus.odeSolving.BulirschStoer
 
step(DoubleArrayParametrized, DoubleArrayValued, double[], double[], double[], double, double[], double[], double[][]) - Static method in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
stepSize - Variable in class numericalMethods.calculus.odeSolving.RungeKutta
 
stepSize - Variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
stepSize - Variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
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.
StereoCupRimClassifier - class stereodisk.StereoCupRimClassifier.
Stereo disk photograph cup and rim classifier.
StereoCupRimClassifier() - Constructor for class stereodisk.StereoCupRimClassifier
 
stereoDifference - Static variable in class VolumeJ.VJRenderViewStereo
 
stereodisk - package stereodisk
 
StereoDiskAnalyzer - class stereodisk.StereoDiskAnalyzer.
Stereo disk photograph analysis.
StereoDiskAnalyzer() - Constructor for class stereodisk.StereoDiskAnalyzer
 
StereoDiskANNMaker - class stereodisk.StereoDiskANNMaker.
Stereo disk photograph analysis.
StereoDiskANNMaker() - Constructor for class stereodisk.StereoDiskANNMaker
 
StereoDiskANNTester - class stereodisk.StereoDiskANNTester.
Stereo disk photograph analysis.
StereoDiskANNTester() - Constructor for class stereodisk.StereoDiskANNTester
 
StereoDiskAutomaticAligner - class stereodisk.StereoDiskAutomaticAligner.
Aligns all optic disk stereo pair stacks in a directory automatically using MI registration.
StereoDiskAutomaticAligner() - Constructor for class stereodisk.StereoDiskAutomaticAligner
 
StereoDiskConventions - class stereodisk.StereoDiskConventions.
Class with defaults and conventions for stereo disk file size, names, directories, etc.
StereoDiskConventions() - Constructor for class stereodisk.StereoDiskConventions
 
StereoDiskFeatureConverter - class stereodisk.StereoDiskFeatureConverter.
Stereo disk feature creation.
StereoDiskFeatureConverter() - Constructor for class stereodisk.StereoDiskFeatureConverter
 
StereoDiskGroundTruthAnalyzer - class stereodisk.StereoDiskGroundTruthAnalyzer.
Analyzes performance of different observers verus ground truth.
StereoDiskGroundTruthAnalyzer() - Constructor for class stereodisk.StereoDiskGroundTruthAnalyzer
 
StereoDiskGroundTruthConverter - class stereodisk.StereoDiskGroundTruthConverter.
Saves the ground truth classification images as a stack with name -. for each observer.
StereoDiskGroundTruthConverter() - Constructor for class stereodisk.StereoDiskGroundTruthConverter
 
StereoDiskIxConverter - class stereodisk.StereoDiskIxConverter.
Stereo disk photograph analysis.
StereoDiskIxConverter() - Constructor for class stereodisk.StereoDiskIxConverter
 
StereoDiskPGMConverter - class stereodisk.StereoDiskPGMConverter.
Stereo disk converter.
StereoDiskPGMConverter() - Constructor for class stereodisk.StereoDiskPGMConverter
 
StereoDiskPGMToFeatureConverter - class stereodisk.StereoDiskPGMToFeatureConverter.
Converts a directory of PGM files to a multi image TIFF file with a specific order (depends on directory.list) Copyright (c) 1999-2004, Michael Abramoff.
StereoDiskPGMToFeatureConverter() - Constructor for class stereodisk.StereoDiskPGMToFeatureConverter
 
StereoDiskROC - class stereodisk.StereoDiskROC.
Stereo disk photograph analysis.
StereoDiskROC() - Constructor for class stereodisk.StereoDiskROC
 
StereoDiskSlideCropper - class stereodisk.StereoDiskSlideCropper.
Evaluates ground truth from different observers.
StereoDiskSlideCropper() - Constructor for class stereodisk.StereoDiskSlideCropper
 
stereoFilter - Static variable in class knn.FeatureComputer
 
StereoFilterBank - class knn.StereoFilterBank.
This class implements a stereo filterbank, i.e.
StereoFilterBank() - Constructor for class knn.StereoFilterBank
 
StereoFilterBank(float[], float[]) - Constructor for class knn.StereoFilterBank
 
stim - Variable in class retina.PCAWindow
 
STIM_BARWIDTH - Static variable in class retina.ScriptProcessor
 
STIM_CHECKERSIZE - Static variable in class retina.ScriptProcessor
 
STIM_IDLE - Static variable in class retina.ScriptProcessor
 
STIM_ISOLUMINANCE - Static variable in class retina.ScriptProcessor
 
STIM_RANDOMBLOCK - Static variable in class retina.ScriptProcessor
 
STIM_TYPE - Static variable in class retina.ScriptProcessor
 
stimuli - Variable in class retina.OIDProcessor
 
stimulus - Variable in class retina.OIDHeader
 
stimulusDescriptor - Variable in class retina.OIDProcessor
 
stimulusEndFrame - Variable in class retina.OIDHeader
 
stimulusMasks - Static variable in class retina.OIDroiAnalyzer
 
STIMULUSOFFSET - Static variable in class retina.RetinalImage
On the last line, this is used as stimulus flag (0=off, 1=on).
stimulusStartFrame - Variable in class retina.OIDHeader
 
stimulusStatus - Variable in class retina.OIDWindow
 
streamToStack() - Method in class va.VAInterface
 
string - Variable in class io.FileAndString
 
stringToCycles(String) - Static method in class numericalMethods.algebra.group.Permutation
Hands back an int[][] coded by a string.
stringToIntArray(String) - Static method in class numericalMethods.algebra.group.Permutation
Hands back an integer array coded by a string.
stringToIntArray(String, int[]) - Static method in class numericalMethods.algebra.group.Permutation
Hands back an integer array coded by a string.
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[], double) - 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
 
subFactorial(int) - Static method in class numericalMethods.algebra.group.Permutation
subFactorial(n+1)=!(n+1)=n*(!n+!(n-1))=[n!/E].
subject - Variable in class retina.OIDHeader
 
submean(float[][], int) - Method in class bijnum.BIJgifa
Computes the mean of the submatrices of a MxN matrix F.
subsample(float[][], int) - Static method in class stereodisk.StereoDiskAnalyzer
Sample every distance elements from set.
subsample(float[], int) - Static method in class stereodisk.StereoDiskAnalyzer
Sample every distance elements from set.
subset(float[][][], int[][]) - Static method in class stereodisk.StereoDiskAnalyzer
Select the subset of pixels (indicated by indices), from set.
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[][]) - Static method in class stereodisk.StereoDiskAnalyzer
Select the subset of pixels (indicated by indices), from set.
subset(float[][], int[][]) - Static method in class stereodisk.StereoDiskIxConverter
Smart sampler.
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.
subset(int[]) - Method in class knn.Features
Return a MxN float[][] matrix with a subset of the current Q features (each N in length), i.e.
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 - Static variable in class retina.OIDProcessor
 
SUBTRACT - Static variable in class retina.OIDAnalysis
 
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(double[]) - Static method in class numericalMethods.calculus.integration.NewtonCotes
 
sum(float[]) - Static method in class bijnum.BIJstats
sum(1) computes summation of all values in vector v.
sum(float[][]) - Static method in class bijnum.BIJstats
sum(1) computes summation of all values in matrix m.
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.
svd() - Method in class Jama.Matrix
Singular Value Decomposition
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
 
swap(int) - Method in class net.sourceforge.jannealer.Schedule
Swapping utility
sweeps - Variable in class bijnum.BIJJacobi
 
sweeps() - Method in class bijnum.Jacobi
Deprecated.  
sweeps() - Method in class bijnum.BIJJacobi
 

T

t - Variable in class numericalMethods.calculus.integration.ExampleIntegration.F
 
t - Variable in class numericalMethods.calculus.minimizing.nmLineND
 
t - Variable in class numericalMethods.calculus.minimizing.Sin
 
t - Variable in class numericalMethods.calculus.minimizing.Cos
 
t - Variable in class numericalMethods.function.util.AbstractValueCacher
 
t - Variable in class numericalMethods.function.util.AbstractValueCacher.Key
 
table2x2(float[], float[], int) - Static method in class bijnum.BIJstats
Make a 2x2 table for the observations obs0 and obs1, where an observation c is taken as correct.
tablenxn(float[], float[], int) - Static method in class bijnum.BIJstats
Make a nxn confusion matrix for the observations obs0 and obs1, for n classes.
takeVotes(byte[][]) - Static method in class stereodisk.StereoDiskGroundTruthConverter
From an array of image classifications, take the votes for each pixel and return a single image with each pixel classified as the class that had the most votes.
takeVotes(byte[][], int, int) - Static method in class stereodisk.StereoDiskGroundTruthConverter
From an array of image classifications, take the votes for each pixel and return a single image with the binned pixel classified as the class that had the most votes.
takeVotes(float[][]) - Static method in class stereodisk.StereoDiskGroundTruthAnalyzer
From an array of image classifications, take the votes for each pixel and return a single image with each pixel classified as the class that had the most votes.
tau - Variable in class FlowJ.FlowJLucas
 
tempArr - Variable in class bijnum.BIJfht
 
temperature - Variable in class net.sourceforge.jannealer.AnnealingScheme
 
test() - Static method in class bijfit.GeneralLinearLeastSquares
 
test() - Static method in class bijnum.BIJmatrix
 
TestAnneal - class net.sourceforge.jannealer.test.TestAnneal.
shows how to invoke the annealing code using an example from JSimul
TestAnneal() - Constructor for class net.sourceforge.jannealer.test.TestAnneal
 
TestAXB - class numericalMethods.algebra.linear.solve.TestAXB.
 
TestAXB() - Constructor for class numericalMethods.algebra.linear.solve.TestAXB
 
TestChebyshevApproximation - class numericalMethods.calculus.functionApproximation.TestChebyshevApproximation.
Test class for ChebyshevApproximation.
testCheckbox - Variable in class VolumeJ.VJUserInterface
 
TestCholesky - class numericalMethods.algebra.linear.decompose.TestCholesky.
 
TestCholesky() - Constructor for class numericalMethods.algebra.linear.decompose.TestCholesky
 
TestClausen - class numericalMethods.calculus.specialFunctions.TestClausen.
Compares values of Clausen.cl2(double x) and Clausen.CATALAN with the corresponding values obtained with a computer algebra system.
TestDeterminant - class numericalMethods.algebra.linear.TestDeterminant.
 
TestDeterminant() - Constructor for class numericalMethods.algebra.linear.TestDeterminant
 
TestExactLLL - class numericalMethods.geometry.latticeReduction.TestExactLLL.
 
TestExactLLL() - Constructor for class numericalMethods.geometry.latticeReduction.TestExactLLL
 
TestGamma - class numericalMethods.calculus.specialFunctions.TestGamma.
 
TestGamma() - Constructor for class numericalMethods.calculus.specialFunctions.TestGamma
 
TestHouseholder - class numericalMethods.algebra.linear.decompose.TestHouseholder.
 
TestHouseholder() - Constructor for class numericalMethods.algebra.linear.decompose.TestHouseholder
 
testing - Static variable in class stereodisk.StereoDiskAnalyzer
Obtain a training or test set (depending on train) as an MxN vector where N is number of features and M is the number of subsampled pixels in all images.
TestInversion - class numericalMethods.algebra.linear.TestInversion.
 
TestInversion() - Constructor for class numericalMethods.algebra.linear.TestInversion
 
testKNN(BIJknn, String, String[], String) - Static method in class stereodisk.StereoDiskAnalyzer
Test a kNN classifier with a test set in names (the odd images), and the ground truth as classification vectors.
TestLLL - class numericalMethods.geometry.latticeReduction.TestLLL.
 
TestLLL() - Constructor for class numericalMethods.geometry.latticeReduction.TestLLL
 
TestLR - class numericalMethods.algebra.linear.decompose.TestLR.
 
TestLR() - Constructor for class numericalMethods.algebra.linear.decompose.TestLR
 
TestLXB - class numericalMethods.algebra.linear.solve.TestLXB.
 
TestLXB() - Constructor for class numericalMethods.algebra.linear.solve.TestLXB
 
TestMatrix - class Jama.test.TestMatrix.
TestMatrix tests the functionality of the Jama Matrix class and associated decompositions.
TestMatrix() - Constructor for class Jama.test.TestMatrix
 
TestNewtonCotes - class numericalMethods.calculus.integration.TestNewtonCotes.
 
TestNewtonCotes() - Constructor for class numericalMethods.calculus.integration.TestNewtonCotes
 
TestPLR - class numericalMethods.algebra.linear.decompose.TestPLR.
 
TestPLR() - Constructor for class numericalMethods.algebra.linear.decompose.TestPLR
 
TestQR - class numericalMethods.algebra.linear.decompose.TestQR.
 
TestQR() - Constructor for class numericalMethods.algebra.linear.decompose.TestQR
 
TestRXB - class numericalMethods.algebra.linear.solve.TestRXB.
 
TestRXB() - Constructor for class numericalMethods.algebra.linear.solve.TestRXB
 
testsin(float[]) - Static method in class bijnum.BIJfft
 
TestTridiagonal - class numericalMethods.algebra.linear.decompose.TestTridiagonal.
 
TestTridiagonal() - Constructor for class numericalMethods.algebra.linear.decompose.TestTridiagonal
 
text - Variable in class retina.OIDWindow
 
textarea - Variable in class io.OpenPreviewDialog
 
textEpochLength - Variable in class retina.OIDReconstructor
 
textFieldInitialFrameRate - Variable in class va.VAInterface
 
textFieldInitialFrames - Variable in class va.VAInterface
 
textFieldPostFrameRate - Variable in class va.VAInterface
 
textFieldPostFrames - Variable in class va.VAInterface
 
tgradientKernel - Variable in class FlowJ.FlowJLucas
 
theta - Variable in class VolumeJ.VJProjection
Angle (in degrees) of each projection image.
thetas - Variable in class knn.FilterBank
 
thetaSet(int) - Static method in class knn.FilterBank
Return a set of good filter orientations (thetas) for filters of order.
ThreadCompression - class va.ThreadCompression.
A thread that compresses frame on the fly.
ThreadCompression(VAInterface, VideoWatch, double, int, double, int, int, int) - Constructor for class va.ThreadCompression
 
threshField - Variable in class bd.BDUserInterface
 
threshold - Variable in class VolumeJ.VJClassifierIsosurface
 
threshold - Variable in class VolumeJ.VJClassifierLevoy
 
threshold - Static variable in class VolumeJ.VJUserInterface
 
threshold - Variable in class registration.HoughTransform
The edge threshold.
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.
time - Variable in class retina.OIDHeader
 
timecourseAnalysis(int, float[][], float[][][][], float[][], float[][], int, int, int, float[][], int, int) - Static method in class retina.OIDAnalysis
Timecourse analysis using masks over all frames.
timecourseBeatAnalysis(float[][], float[][], int, int, int, int, int, float[][]) - Static method in class retina.OIDAnalysis
Do timecourse analysis of the area that is 1 in masks[0] for each condition relative to a baseline area that is 1 in masks[0], averaged between baselineStart and baselineEnd.
TimedAcquisition - class va.TimedAcquisition.
A thread that acquires a video sequence and at two different frame rates.
TimedAcquisition(VAInterface, VideoWatch, double, int, double, int, int, int) - Constructor for class va.TimedAcquisition
 
TIMEFRAME - Static variable in class retina.ScriptProcessor
 
timerPhase - Variable in class va.VAInterface
 
times(double) - Method in class Jama.Matrix
Multiply a matrix by a scalar, C = s*A
times(double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix multiplication: A * B = C.
times(double[][], double[][], double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix multiplication: A * B = C.
times(double[][], double[][], double[], double[], double[], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix - vector multiplication: A * b = c.
times(double[][], double[][], double, double, double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs A * b = b * A = C.
times(double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix - vector multiplication: A * b = c.
times(double[][], double, double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs A * b = b * A = C.
times(double[][], int[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix multiplication: A * B = C.
times(double[][], int[], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix - vector multiplication: A * b = c.
times(double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs dot product.
times(double[], double[][], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs vector - matrix multiplication: a^t * B = c^t.
times(double[], double[], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs vector - vector multiplication: a * b^t = C.
times(double[], double[], double[][], double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix - vector multiplication: b * A = c.
times(double[], double[], double, double, double[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector.
times(double[], double[], int, double[], double[], int, double[], double[]) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
times(double[], double[], int, double[], double[], int, double[], double[], int) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
times(double[], double, double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector.
times(double[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs dot product.
times(double[], int[][], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs vector - matrix multiplication: a^t * B = c^t.
times(double[], int[], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs vector - vector multiplication: a * b^t = C.
times(int[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix multiplication: A * B = C.
times(int[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix - vector multiplication: A * b = c.
times(int[][], double, double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs A * b = b * A = C.
times(int[][], int[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix multiplication: A * B = C.
times(int[][], int[][], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix multiplication: A * B = C.
times(int[][], int[], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix - vector multiplication: A * b = c.
times(int[][], int[], int[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs matrix - vector multiplication: A * b = c.
times(int[][], int, int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs A * b = b * A = C.
times(int[], double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs dot product.
times(int[], double[][], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs vector - matrix multiplication: a^t * B = c^t.
times(int[], double[], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs vector - vector multiplication: a * b^t = C.
times(int[], double, double[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector.
times(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
 
times(int[], int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Performs dot product.
times(int[], int[][], double[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs vector - matrix multiplication: a^t * B = c^t.
times(int[], int[][], int[]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs vector - matrix multiplication: a^t * B = c^t.
times(int[], int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Composes two permutations.
times(int[], int[], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Performs vector - vector multiplication: a * b^t = C.
times(int[], int, int[]) - Static method in class numericalMethods.algebra.linear.VectorOperations
Scales vector.
times(Matrix) - Method in class Jama.Matrix
Linear algebraic matrix multiplication, A * B
timesEquals(double) - Method in class Jama.Matrix
Multiply a matrix by a scalar in place, A = s*A
timesFun(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
 
timesFun(int[], int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Returns p1[p2[i]] in result.
timesInverse(int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
 
timesInverse(int[], int[], int[]) - Static method in class numericalMethods.algebra.group.Permutation
Composes two permutations as functions and returns the permutation (contra-functional) notation in result.
TINY - Static variable in class numericalMethods.calculus.minimizing.nmBracket
 
TINY - Static variable in class numericalMethods.calculus.odeSolving.RungeKuttaFehlberg
 
TINY - Static variable in class numericalMethods.calculus.odeSolving.BulirschStoer
 
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.
tofloat(double[]) - Static method in class bijnum.BIJutil
 
toGrid(float[], float[]) - Static method in class FlowJ.FlowJFlow
Translate to grid coordinates.
TOL - Static variable in class numericalMethods.calculus.minimizing.LineNDDBrent
 
TOL - Static variable in class numericalMethods.calculus.minimizing.nmPowell
 
TOL - Static variable in class numericalMethods.calculus.minimizing.nmLineNDBrent
 
TOL - Static variable in class numericalMethods.calculus.specialFunctions.TestClausen
 
tolerance - Variable in class net.sourceforge.jannealer.AnnealingScheme
 
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
 
toMatrix() - Method in class knn.Features
 
toMatrix(Vector) - Static method in class knn.Feature
 
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 bijfit.DesignMatrix
 
toString() - Method in class bijnum.Jacobi
Deprecated.  
toString() - Method in class bijnum.BIJJacobi
 
toString() - Method in class knn.Feature
 
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 registration.RegisterFFTHessian
 
toString() - Method in class registration.LocatedCircle
 
toString() - Method in class registration.RegisterMI
 
toString() - Method in class registration.RegisterFFT
 
toString() - Method in class retina.OIDAnalyzer
 
toString() - Method in class retina.OIDMapsFitter
 
toString() - Method in class retina.OIDroiAnalyzer
 
toString() - Method in class retina.OIDroiTCAnalyzer
 
toString() - Method in class retina.OIDPCAAnalyzer
 
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(double[], double[], int) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
toString(double[], double[], int, double) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
toString(double[], double[], int, int) - Static method in class numericalMethods.algebra.polynomial.ComplexLaurentPolynomial
 
toString(double[], double[], int, int, double) - Static method in class numericalMethods.algebra.polynomial.ComplexPolynomial
 
toString(double[], double[], int, int, double) - Static method in class numericalMethods.algebra.polynomial.ComplexLaurentPolynomial
 
toString(float[]) - Static method in class bijnum.BIJutil
 
toString(float[][]) - Static method in class bijnum.BIJutil
 
toString(int) - Method in class knn.Features
 
toString(int[]) - Static method in class numericalMethods.algebra.group.Permutation
Describe toString method here.
toString(int[][]) - 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(int, String) - Method in class knn.FilterBank
Return a descriptive String for this filter number.
toString(int, String) - Method in class knn.StereoFilterBank
Return a descriptive String for this filter number.
toString(int, String) - Method in class knn.DOGFilterBank
Return a descriptive String for this filter number.
toString(short[]) - Static method in class bijnum.BIJShortMatrix
 
toString(String) - Static method in class knn.StereoFilterBank
Return a descriptive String for a depth map number.
toString(Vector) - Static method in class knn.Feature
 
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.
toVector() - Method in class knn.Feature
 
toVector(int) - Method in class knn.Features
 
tptest(double[], double[]) - Static method in class bijnum.BIJstats
Perform paired Student's t-test on two data sets data1 and data2, with the the t values into t and the probabilities into prob.
trace() - Method in class Jama.Matrix
Matrix trace.
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
 
training - Static variable in class stereodisk.StereoDiskAnalyzer
 
trainKNN(String, String[], String) - Static method in class stereodisk.StereoDiskAnalyzer
Train a KNN classifier with the features in names as feature vectors, and the ground truth in gtname as classification vectors.
transform(double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.Tridiagonal
Transforms symmetric matrix A into triadiagonal form which is returned in T.
transform(double[][], double[][], double[], double[]) - Static method in class numericalMethods.algebra.linear.decompose.Tridiagonal
Transforms symmetric matrix A into triadiagonal form.
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() - Method in class Jama.Matrix
Matrix transpose.
transpose(byte[][]) - Static method in class bijnum.BIJmatrix
Compute the transpose of a matrix m.
transpose(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Transpose m and store the result in trans matrix.
transpose(float[][]) - Static method in class bijnum.BIJmatrix
Compute the transpose of a matrix m.
transpose(int[][], int[][]) - Static method in class numericalMethods.algebra.linear.MatrixOperations
Transpose m and store the result in trans matrix.
transposeR(float[], int) - Method in class bijnum.BIJfht
 
trb - Variable in class VolumeJ.VJVoxelLoc
 
trf - Variable in class VolumeJ.VJVoxelLoc
 
trianglewave(double, double, double, double, double) - Static method in class retina.OIDAnalysis
Double triangle wave.
trianglewave(int, int, int, double, double, double) - Static method in class retina.OIDAnalysis
Double triangle wave in terms of frames.
triangular(double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.Unmerge
Separates the left and right triangular part out of a merged real matrix.
triangular(double[][], double[][], double[][], double[][]) - Static method in class numericalMethods.algebra.linear.decompose.Unmerge
Separates the left and right triangular part out of a merged complex matrix.
triangulate(double[]) - Static method in class numericalMethods.geometry.meshGeneration.ruppert.Delaunay
 
triangulate(double[][][], double) - Method in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
Tridiagonal - class numericalMethods.algebra.linear.decompose.Tridiagonal.
Transforms a symmetric matrix into triadiagonal form.
triTable - Static variable in class numericalMethods.geometry.hyperSurface.MarchingCubes
 
Trivial - class net.sourceforge.jannealer.test.Trivial.
solve (x-3)^2=0 using simulated annealing
Trivial() - Constructor for class net.sourceforge.jannealer.test.Trivial
 
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.
truncatedDifferenceAnalysis(BIJpca, int, int, int, int, int, float[], int, double) - Static method in class retina.OIDAnalysis
Do truncated difference analysis (averaged for each condition) in a separately.
truncatedSequenceAnalysis(BIJpca, int, int, int, int, int, float[], int, double) - Static method in class retina.OIDAnalysis
Performs truncated sequence analysis, i.e.
ttest(double[], double[]) - 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.
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.
TupleSequences - class numericalMethods.util.TupleSequences.
This class provides utilities for arrays as static methods with a special structure, namely for sequences of tuples with a common size, the tupleSize.
TupleSequences() - Constructor for class numericalMethods.util.TupleSequences
 
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

uminus() - Method in class Jama.Matrix
Unary minus
UNDERFLOW_LIMIT - Static variable in class bijnum.BIJJacobi
 
UNIQUECONDS - Static variable in class retina.ScriptProcessor
 
UNIQUECONDSINFILE - Static variable in class retina.ScriptProcessor
 
unitvar() - Method in class knn.Feature
 
unitvar(float[]) - Static method in class bijnum.BIJstats
Make a new vector of v that has zero mean and unit variance.
unitvar(float[][]) - Static method in class bijnum.BIJstats
Make m unit variance and zero mean with respect to all elements of m.
unitvars(float[][], double[], double[]) - Static method in class stereodisk.StereoDiskANNTester
Make unit variance all elements in m columnwise.
unitvars(float[][], double[], double[]) - Static method in class stereodisk.StereoDiskROC
Make unit variance all elements in m columnwise.
Unmerge - class numericalMethods.algebra.linear.decompose.Unmerge.
Seperates merged matrices.
Unmerge() - Constructor for class numericalMethods.algebra.linear.decompose.Unmerge
 
unrole(double[], double[], int) - Static method in class numericalMethods.util.Arrays
Returns an array containing numOfTimes copies of the contens of values.
unrole(float[], float[], int) - Static method in class numericalMethods.util.Arrays
Returns an array containing numOfTimes copies of the contens of values.
unrole(int[], int[], int) - Static method in class numericalMethods.util.Arrays
Returns an array containing numOfTimes copies of the contens of values.
updateCosAngle() - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
updateEdge(double[]) - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
updateLength() - Method in class numericalMethods.geometry.meshGeneration.util.AngleOptimization2D
 
userSelectImagePlus(String) - Method in class retina.PCAWindow
Allows user to select an image from all open images in a dialog.
Util - class net.sourceforge.jannealer.test.Util.
Test classes utilities
Util() - Constructor for class net.sourceforge.jannealer.test.Util
 
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
 
va - package va
 
vaInterface - Variable in class va.TimedAcquisition
 
vaInterface - Variable in class va.ThreadCompression
 
VAInterface - class va.VAInterface.
User interface for Video Angiography.
VAInterface() - Constructor for class va.VAInterface
Open a new VAInterface.
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.
validFileDescription(File) - Method in class retina.OIDReconstructor
Modify the name of the file if you want.
validFiles - Variable in class io.OpenPreviewDialog
 
value - Static variable in class FlowJ.FlowJSpotNoise
 
value - Variable in class numericalMethods.calculus.minimizing.Quadric
 
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.
values - Variable in class registration.HoughTransform
 
var(double[]) - Static method in class bijnum.BIJstats
Compute variance of all elements in vector v.
var(float[]) - Static method in class bijnum.BIJstats
Compute variance of all elements in vector v.
variance - Variable in class bd.BDUserInterface
 
varianceSpectrum() - Method in class bijnum.BIJpca
Compute the accumulated variance spectrum.
VBARHEIGHT - Static variable in class retina.ScriptProcessor
 
VBARWIDTH - Static variable in class retina.ScriptProcessor
 
vector - Variable in class knn.Feature
 
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.
VectorOperations - class numericalMethods.algebra.linear.VectorOperations.
This class handles the basic operations with vectors.
verbosity - Variable in class retina.ScriptProcessor
 
VERSION - Static variable in class VolumeJ.VJUserInterface
 
VERSION - Static variable in class VolumeJ.VJSurfaceJ
 
VERSION - Static variable in class va.VAInterface
 
vertices(int, int, int) - Static method in class VolumeJ.VJCell
Compute the vertex coordinates of a cell at x, y, z.
VideoAcq - class va.VideoAcq.
A thread that acquires a video sequence and saves to disk using IMAQ calls.
VideoAcq(VAInterface) - Constructor for class va.VideoAcq
 
videoImp - Variable in class va.VAInterface
 
videoPixels - Variable in class va.VideoWatch
 
videoPixels - Variable in class va.VideoAcq
 
videoProcessor - Variable in class va.VAInterface
 
VideoWatch - class va.VideoWatch.
A thread that continously updates the video frame, and stores the images for acquisition if requested.
VideoWatch(VAInterface) - Constructor for class va.VideoWatch
 
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.