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

A

a - Variable in class bijnum.BIJJacobi

The matrix of which you want to compute E.

a - Variable in class bijnum.BIJpca

The matrix of images.

a - Variable in class registration.SearchMI

Two images.

abs(float[]) - Static method in class bijnum.BIJmatrix

Return a vector with the absolutes of all elements in vector v.

accept(File) - Method in class retina.AcceptOID

accept(File, String) - Method in class retina.FileNameFilterAcceptOID

AcceptOID - Class in retina

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 multiclass 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.PVCAMInterface

acqFinished() - Method in class va.VAInterface

actionPerformed(ActionEvent) - Method in class Align_Stereo

React to action e.

actionPerformed(ActionEvent) - Method in class bd.BDUserInterface

actionPerformed(ActionEvent) - Method in class FlowJ.FlowJUserInterface

actionPerformed(ActionEvent) - Method in class Nearest

actionPerformed(ActionEvent) - Method in class retina.OIDReconstructor

actionPerformed(ActionEvent) - Method in class retina.OIDWindow

actionPerformed(ActionEvent) - Method in class retina.PCAWindow

Act upon buttons pressed.

actionPerformed(ActionEvent) - Method in class stimulator.StimulusJInterface

actionPerformed(ActionEvent) - Method in class va.PVCAMInterface

actionPerformed(ActionEvent) - Method in class va.VAInterface

actionPerformed(ActionEvent) - Method in class VolumeJ.VJUserInterface

React to action e.

ACTIVATE - Static variable in class stimulator.CCDcontrol

add(float[][], float[]) - Method in class bijnum.BIJknn

Add extra data and classification to this knn.

add(float[], float, float[]) - Static method in class bijnum.BIJmatrix

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[], double) - Static method in class bijnum.BIJmatrix

Add a scalar to all entries in a vector m in place.

add(float[][], double) - Static method in class bijnum.BIJmatrix

Add a scalar to all entries in a matrix m in place.

add(float[][], float[][]) - Static method in class bijnum.BIJmatrix

Add (elements in) a matrix b to a matrix a.

add(short[], float) - Static method in class bijnum.BIJShortMatrix

Add a scalar to all entries in a matrix.

add(Vector<Feature>, Feature[]) - Static method in class features.Feature

Add the elements in newfeatures to features.

add(Vector<Feature>, Feature) - Static method in class features.Feature

Add the elements in newfeatures to features.

add(Vector<Feature>, Vector<Feature>) - Static method in class features.Feature

Add the elements in newfeatures to features.

add(Feature[]) - Method in class features.Features

Add the elements in newfeatures to features.

add(Vector<Feature>) - Method in class features.Features

Add the elements in newfeatures to features.

add(SSD, SSD) - Method in class FlowJ.SSD

add(VolumeFloat) - Method in class volume.VolumeFloat

addElements(double[], double[], double[]) - Static method in class bijnum.BIJmatrix

addElements(float[], float[], float[]) - Static method in class bijnum.BIJmatrix

addElements(float[], float[]) - Static method in class bijnum.BIJmatrix

addPanel() - Method in class retina.PCAWindow

Add the GUI items to this Window.

addSlice(String, float[], ImageStack) - Static method in class bijnum.BIJutil

Add an image to a ImageStack of FloatProcessors.

addSlice(String, byte[], ImageStack) - Static method in class bijnum.BIJutil

Add an image to a ImageStack of FloatProcessors.

addSlice(String, short[], ImageStack) - Static method in class bijnum.BIJutil

Add an image to a ImageStack of FloatProcessors.

addSlice(String, int[], ImageStack) - Static method in class bijnum.BIJutil

Add an image to a ImageStack of FloatProcessors.

addSlice(String, ImageProcessor, ImageStack) - Static method in class bijnum.BIJutil

Add an image to a ImageStack of FloatProcessors.

adjustmentValueChanged(AdjustmentEvent) - Method in class retina.OIDWindow

Inherited from StackWindow

adjustmentValueChanged(AdjustmentEvent) - Method in class retina.PCAWindow

User has moved the slider on the StackWindow.

advanceInit(VJCell, double, double, double) - Method in class VJiso.VJBinaryShell

Initialization of depth search routine.

advanceInit(VJCell, double, double, double) - Method in class VolumeJ.VJBinaryShell

Initialization of depth search routine.

advancePrepare(double, double, double) - Method in class VJiso.VJBinaryShell

Prepare surface search for a ray with a specific direction vector.

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 VJiso.VJBinaryShell

Advance a cell to a surface along the ray.

advanceToSurface(VJCell) - Method in class VolumeJ.VJBinaryShell

Advance a cell to a surface along the ray.

advanceToSurfaceTracing(VJCell) - Method in class VJiso.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.

aggregateRegistration - Variable in class retina.OIDProcessor

Registration parameters for aggregate, null if no registration was performed.

AGGREGATESAVE - Static variable in class scripts.ScriptProcessor

Align_Stereo - Class in <Unnamed>

This class helps to align two slices (presumably a stereo pair) in a stack.

Align_Stereo() - Constructor for class Align_Stereo

alignmentTimecourseAnalysis(float[][], int, int) - Static method in class retina.OIDAnalysisMethods

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 of3d.OF3DSpot

alpha - Variable in class VolumeJ.VJAlphaColor

alphacolor(VJValue, VJGradient) - Method in class of3d.OFClassifier

alphacolor(FlowJValue, VJGradient) - Method in class of3d.OFClassifier

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.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.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.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.OFClassifierScintillansIxLT0

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.OFClassifierScintillansNoStatic

Classify a flow based on the flow vector, and whether or not a static voxel is present, into a VJAlphaColor.

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) - Method in class VolumeJ.VJClassifier

This method can be overloaded as necessary.

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.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) - Method in class VolumeJ.VJClassifierLevoy

Slice view classification.

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(VJrgbValue, VJGradient) - Method in class VolumeJ.VJClassifierRGB

alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierValue

Classify the interpolated voxel value into a VJAlphaColor.

analysisTime - Variable in class retina.OIDamplitudeAnalyzer

Moment after start of stimulus when you want to examine amplitude of signal.

analyze(float[][], int, String, String) - Method in class retina.OIDamplitudeAnalyzer

Analyze 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[][], int, String, String) - Method in class retina.OIDAverageAnalyzer

Analyze a series of OID frames a.

analyze(float[][], float[][], int, String, String) - Method in interface retina.OIDBaseAnalyzer

analyze(float[][], int, String, String) - Method in class retina.OIDbaselineAnalyzer

Analyze a series of OID frames a.

analyze(float[][], float[][], int, String, String) - Method in class retina.OIDffAllAnalyzer

Analyze a series of OID frames a.

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.OIDPCAAnalyzer

Analyze a series of OID frames a.

analyze(float[][], float[][], int, String, String) - Method in class retina.OIDroiAnalyzer

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[][], float[][], int, String, String) - Method in class retina.OIDROItimecourseAnalyzer

Analyze a series of OID frames a.

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.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 - Static variable in class scripts.ScriptProcessor

analyze(String[], Point2D.Float[], float[][], String) - Static method in class stereo.StereoAnalyzer

ANALYZE_AMPLITUDE - Static variable in class scripts.ScriptProcessor

ANALYZE_AUTOSCALING - Static variable in class scripts.ScriptProcessor

ANALYZE_BAG - Static variable in class scripts.ScriptProcessor

ANALYZE_CONDS - Static variable in class scripts.ScriptProcessor

ANALYZE_FIRSTFRAME - Static variable in class scripts.ScriptProcessor

ANALYZE_FOVEAX - Static variable in class scripts.ScriptProcessor

ANALYZE_FOVEAY - Static variable in class scripts.ScriptProcessor

ANALYZE_MASKFILE - Static variable in class scripts.ScriptProcessor

ANALYZE_PCA - Static variable in class scripts.ScriptProcessor

ANALYZE_REGISTER - Static variable in class scripts.ScriptProcessor

ANALYZE_REGISTER_ROISIZE - Static variable in class scripts.ScriptProcessor

ANALYZE_REGISTER_ROIX - Static variable in class scripts.ScriptProcessor

ANALYZE_REGISTER_ROIY - Static variable in class scripts.ScriptProcessor

ANALYZE_ROI - Static variable in class scripts.ScriptProcessor

ANALYZE_ROITC - Static variable in class scripts.ScriptProcessor

ANALYZE_START - Static variable in class scripts.ScriptProcessor

ANALYZE_TIMECOURSE - Static variable in class scripts.ScriptProcessor

ANALYZE_USECOND - Static variable in class scripts.ScriptProcessor

analyzeProbabilities(float[][], float[][], int, Vector) - Static method in class stereodisc.Analyzer

Determine the probabilities that a pixelfeature can differentiate between two classes for all classes and all features.

Analyzer - Class in stereodisc

Stereo disk photograph analysis.

Analyzer() - Constructor for class stereodisc.Analyzer

AngiographAnalyzer - Class in retina

Angiograph analyzer.

AngiographAnalyzer() - Constructor for class retina.AngiographAnalyzer

ANN - Class in classifier

API for interface to ANN (Approximate Nearest Neighbor) classification.

ANN() - Constructor for class classifier.ANN

ANNAccuracy - Class in stereodisc

Stereo disk photograph analysis.

ANNAccuracy() - Constructor for class stereodisc.ANNAccuracy

annkEstimates(float[], float[][], int, int, double, float[]) - Static method in class classifier.ANN

annkPriSearch(float[], int, int[], float[], double) - Static method in class classifier.ANN

ANNMapper - Class in stereodisc

Stereo disk photograph analysis.

ANNMapper() - Constructor for class stereodisc.ANNMapper

aroc(int[][], int) - Static method in class bijnum.BIJstats

Determine area under the roc curve for an experiment that gave the frequencies given in the table.

at(int, int, int) - Method in class VolumeJ.VJShape

attenuate(VJShade) - Method in class VolumeJ.VJAlphaColor

ATTR_ACCESS - Static variable in class va.PVCAM

ATTR_AVAIL - Static variable in class va.PVCAM

ATTR_COUNT - Static variable in class va.PVCAM

ATTR_CURRENT - Static variable in class va.PVCAM

ATTR_DEFAULT - Static variable in class va.PVCAM

ATTR_INCREMENT - Static variable in class va.PVCAM

ATTR_MAX - Static variable in class va.PVCAM

ATTR_MIN - Static variable in class va.PVCAM

ATTR_TYPE - Static variable in class va.PVCAM

audioFormatToString(AudioFormat) - Static method in class usbcam.DeviceInfo

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.

AutomaticAligner - Class in stereodisc

Aligns all optic disk stereo pair stacks in a directory automatically using MI registration.

AutomaticAligner() - Constructor for class stereodisc.AutomaticAligner

average(float[], int, int) - Static method in class features.CorrectiveFilters

Compute new image where NaN pixels are replaced with the average of the nearest k pixels.

average(Roi) - Method in class FlowJ.FlowJError

average(Roi) - Method in class FlowJ.FlowJFlow

averageAlpha() - Method in class FlowJ.FlowJFlow

Return the angle of the previously computed average flow.

averageMagnitude() - Method in class FlowJ.FlowJFlow

Return the length of the previously computed average flow.

averageOverVelocity() - Method in class FlowJ.FlowJError

AverageSampleStat(double[][][][]) - Method in class RuggeriEnhanceUp

avg(float[], float[], int, int) - Static method in class bijnum.BIJmulticlass

Compute average of values in vector v of all n classes in v but c

avg(float[], float[], int) - Static method in class bijnum.BIJmulticlass

Compute average of values in vector v of class c.

avg(float[], float[]) - Static method in class bijnum.BIJstats

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(double[]) - Static method in class bijnum.BIJstats

Compute average of all values in vector v.

avg(byte[]) - Method in class ImageBlender_

avgNoExtremes(float[], float) - Static method in class bijnum.BIJstats