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 _

S

S(float[], float[], int, double[], String) - Static method in class features.filterBanks.Stereo

Wrapper for steroe disparity operations.

salgorithm - Static variable in class bd.BlobDetector

sameState() - Method in class stimulator.Cycle

sample(int[]) - Method in class features.Features

Return a new Features with all Feature element arrays containing only the elements in indices.

samples - Static variable in class stereo.StereoPairSplitter

samples - Static variable in class stereo.StereoSegmentation

SampleStatistics(ImageProcessor) - Method in class RuggeriEnhanceUp

sampleTrainingFeatures(String[], int[][]) - Static method in class stereodisc.ANNMapper

Sample the training features names with indices, for all images.

sampleTrainingFeaturesForLeaveOneOut(String[], int[][], int) - Static method in class stereodisc.ANNMapper

Sample the features in names with indices, for all images except exclude.

Saturation - Static variable in class features.color.Channel

save(float[][], int, String, String) - Static method in class retina.OIDPCAAnalyzer

Dump the matrix m as a raw float stack to disk.

save(ImagePlus, String, String) - Static method in class SaveAsSPE_

saveAnalysis(String, String, float[], int, int, String, boolean) - Static method in class retina.OIDDisplayMethods

saveAnalysis(String, String, float[][], int, int, String, boolean) - Static method in class retina.OIDDisplayMethods

saveAnalysis(String, String, float[][][], int, int, String, boolean) - Static method in class retina.OIDDisplayMethods

saveAnalysis(float[][], int, String, String, boolean) - Method in class scripts.ScriptProcessor

Save the analysis in images.

saveAsciiImage(ImagePlus, String, String) - Static method in class PGM_Writer

saveAsObject(String) - Method in class of3d.OF3DFlow

SaveAsSPE_ - Class in <Unnamed>

SaveAsSPE_() - Constructor for class SaveAsSPE_

saveAsTable(float[], String, String) - Method in class scripts.ScriptProcessor

Save the vectors avg, and x as an Excel compatible, tab separated table.

saveAsTable(float[], float[], float[], String, String) - Method in class scripts.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 scripts.ScriptProcessor

Save the vectors avg, below, above, and x as an Excel compatible, tab separated table.

saveAsTable(StringBuffer, String, String) - Method in class scripts.ScriptProcessor

Save the vectors avg, below, above, and x as an Excel compatible, tab separated table.

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

Save vector v as a text file.

saveImagePlusAsTiff(String, String, ImagePlus) - Static method in class bijnum.BIJutil

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

saveRegistrationAsTable(float[], float[], float[], String) - Method in class scripts.ScriptProcessor

Save the vectors with the x, y and rotation registration parameters into a Excel readblae separated file.

saveTimecourse(String, String, float[][], int, int, int) - Static method in class retina.OIDDisplayMethods

Save the timecourse for a as a TIFF file.

saveTimecourse(int, int, int) - Method in class retina.OIDStackWindow

Save the timecourse as a TIFF file.

scale(float[][], double, double, double) - Static method in class bijnum.BIJtransform

Scale a 3-D transformation matrix by sx, sy, sz.

scale(float[][], double, double) - Static method in class bijnum.BIJtransform

Scale a 2-D transformation matrix by sx, sy.

scale(double, double, double) - Method in class VolumeJ.VJMatrix

Scale the coordinate system by sx, sy, sz.

scaleSet(int) - Static method in class features.filterBanks.FilterBank

Return a set of n good scales for scale space.

scaling - Static variable in class stereo.StereoSegmentation

scaling - Static variable in class stereodisc.TIFFFeatureConverter

ScriptProcessor - Class in scripts

Class to process / analyze OID files and directories of OID using a script file.

ScriptProcessor() - Constructor for class scripts.ScriptProcessor

ScriptProcessor(String, String, OIDBaseAnalyzer) - Constructor for class scripts.ScriptProcessor

Create a new ScriptProcessor that can call back to an analyzer.

ScriptProcessor(String, String) - Constructor for class scripts.ScriptProcessor

Create a new OIDFileProcessor to process the control file.

ScriptProcessor(String, String, boolean) - Constructor for class scripts.ScriptProcessor

Create a new OIDFileProcessor to process the control file.

scripts - package scripts

sderiv - Static variable in class bd.BlobDetector

sderiv - Static variable in class FlowJ.FlowJLucas

sderiv - Static variable in class of3d.OF3DLucas

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

Find the k-nearest neighbors of vector v (N dimensional) in dataset and put indices in kIndices, distances in kDistances.

SearchMI - Class in registration

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.

segmentation - package segmentation

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.

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.

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.

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

Compute sensitivities of multiclass test from a confusion matrix matrixnxn.

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.

SEP - Static variable in class stereo.StereoAnalyzer

SEP - Static variable in class stereo.StereoPairSplitter

SEP - Static variable in class stereo.StereoSegmentation

SEPARATE - Static variable in class retina.OIDAnalysisMethods

SEPARATE - Static variable in class retina.OIDProcessor

set(int, int, float, float) - Method in class FlowJ.FlowJFlow

set(int, int, float, float, boolean) - Method in class FlowJ.FlowJFlow

set(Object, int, int, int) - Method in class of3d.OF3DFlow

set(int, double) - Method in class scripts.ScriptProcessor

Set parameter ix to value value.

set(Object, int, int, int) - Method in class VJiso.VJBinaryShell

Set the shell value to a boolean value.

set(Object, int, int, int) - Method in class VJiso.VJThresholdedVolume

Set the threshold value to a boolean value.

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.

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.VolumeFloat

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.VolumeShort

Set the voxel value to a Number.

set(int, int, int, int) - Method in class volume.VolumeShort

Deprecated.

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 VolumeJ.VJThresholdedVolume

Set the threshold value to a boolean value.

setAlpha(float) - Method in class VolumeJ.VJAlphaColor

setAnalyzer(OIDBaseAnalyzer) - Method in class retina.OIDScriptProcessor

setAnalyzer(OIDBaseAnalyzer) - Method in class scripts.ScriptProcessor

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.

setBase(String) - Static method in class stereodisc.Conventions

setCalibration(Calibration) - Method in class FlowJ.FlowJFlow

setClassifier(VJClassifier) - Method in class VolumeJ.VJRenderer

setCutout(VJCutout) - Method in class VolumeJ.VJRenderer

setCycle(Cycle, boolean, int, boolean) - Method in class stimulator.StimScreen

Set the epoch, but do not continue the main loop until prep is okayed.

setD(float) - Method in class VolumeJ.VJPlane

Set the D for the plane equation Ax+By+C+D=0 of this plane

setDatatype(int) - Method in class SpeHeader

setDescription(String) - Method in class VolumeJ.VJRenderer

setDoubleArrayParameter(double[], int) - Method in class registration.SearchMI

Required because implements nmDoubleArrayParametrized.

setEdge(int) - Method in class volume.Volume

Set the edges in the volume beyond which a voxel is not valid.

setExtraInfo(String) - Method in class retina.OIDHeader

setFormat(DataSource, Format) - Static method in class usbcam.DeviceInfo

setFraction(float) - Method in class of3d.OFClassifier

setFraction(double) - Method in class of3d.OFClassifierScintillans

Set the fraction of the flows that are displayed as scintillations.

setHeader(byte[]) - Method in class retina.OIDHeader

setHeader(OIDHeader) - Method in class retina.OIDProcessor

Set the OID header obtained from OID info.

setHeader(byte[]) - Method in class SpeHeader

setHeight(int) - Method in class retina.OIDHeader

setHeight(int) - Method in class SpeHeader

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(Object[]) - Method in class volume.VolumeRGB

Combine the values of s into the index array of this volume.

setIndex(int) - Method in class VolumeJ.VJValue

setIndexed(boolean) - Method in class volume.VolumeShort

setInterpolator(VJInterpolator) - Method in class VolumeJ.VJRenderer

setLUT(byte[], byte[], byte[]) - Method in class VolumeJ.VJClassifier

Set up a user-defined LUT.

setLUT(byte[], byte[], byte[]) - Method in class VolumeJ.VJClassifierLevoy

Set the LUT to a user-defined LUT.

setMap(byte[]) - Method in class stimulator.StimScreen

Set the initialization maps.

setMessage(String) - Method in class VolumeJ.VJRenderer

Set the rendering message.

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.

setProcessing(String) - Method in class retina.OIDHeader

Prepend a modification String to the headerinfo so we know it is the result of processing.

setProperties(int, int, int, String) - Method in class retina.OIDHeader

setProperties(int, int, int, int) - Method in class SpeHeader

setRadius(double) - Method in class registration.LocatedCircle

setRegistration(boolean) - Method in class scripts.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.

setRenderView(VJRenderViewInteractive) - Method in class VolumeJ.VJViewerCanvas

Set the VJRenderViewInteractive instance to process actions.

setRho(float) - Method in class of3d.OFClassifier

setRho(double) - 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.

setStackSize(int) - Method in class retina.OIDHeader

setStackSize(int) - Method in class SpeHeader

setStartTime() - Method in class stimulator.Cycle

Set the display start time for this epoch.

setStaticVolume(Volume) - Method in class of3d.OF3DFlow

Sets a secondary static volume for which the flow has been computed.

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

setThreshold(double) - Method in class bd.BlobDetector

setThreshold(double) - Method in class VolumeJ.VJClassifierIsosurface

setThreshold(double) - Method in class VolumeJ.VJClassifierLevoy

Set center of gradient tent function.

setTransformation(VJMatrix) - Method in class VolumeJ.VJRenderer

Set the transformation matrix of the renderer to m.

setTransformation(VJMatrix, VJMatrix) - Method in class VolumeJ.VJRenderer

Set the transformation matrix of the renderer to m and the special light transformation matrix to correct the light position (should not be influenced by e.g.

setup() - Method in class bd.BDColorSeparator

setup(double) - Method in class bd.BDVarDetector

setup(double, int, int) - Method in class bd.BlobDetector

setup(String, ImagePlus) - Method in class ContrastNorm_Ruggeri

setup(String, ImagePlus) - Method in class Diffusion_

setup(String, ImagePlus) - Method in class Diffusion_4D

setup(String, ImagePlus) - Method in class Find_Disk

setup(String, ImagePlus) - Method in class Find_FOV

setup(String, ImagePlus) - Method in class Frequency_finder

setup(String, ImagePlus) - Method in class GoldFinger_

setup(String, ImagePlus) - Method in class Grid_maker

setup(String, ImagePlus) - Method in class Horiz_Correlator

setup(String, ImagePlus) - Method in class Hough_

setup(String, ImagePlus) - Method in class Hough_Circle

setup(String, ImagePlus) - Method in class Hough_Largest_Circle

setup(String, ImagePlus) - Method in class ImageBlender_

setup(String, ImagePlus) - Method in class Map_MI

setup(String, ImagePlus) - Method in class Map_Timecourse

setup(String, ImagePlus) - Method in class MI_

setup(String, ImagePlus) - Method in class Montage_Cutter

setup(String, ImagePlus) - Method in class MontageCutter_II

setup(String, ImagePlus) - Method in class MontageCutter_III

setup(Volume, VJMatrix) - Method in class of3d.OF3DDeformer

setup() - Method in class of3d.OFClassifierScintillans

setup(String, ImagePlus) - Method in class PCA_

setup(String, ImagePlus) - Method in class Peak_Finder

setup(String, ImagePlus) - Method in class Register_ROI

setup(String, ImagePlus) - Method in class registration.RegisterImageJUtilities

setup(String, ImagePlus) - Method in class Retina_Blobs

setup(String, ImagePlus) - Method in class Retina_Equalize

setup(String, ImagePlus) - Method in class Retina_Register

setup(String, ImagePlus) - Method in class Ruggeri_Enhance_Up

setup(String, ImagePlus) - Method in class Subtract_Mean_Pixel

setup(String, ImagePlus) - Method in class Test_

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.

setupOpacities(double) - Method in class VolumeJ.VJClassifierLevoy

Compute the opacities for a range of voxel values and gradient values.

setVerbosity(int) - Method in class scripts.ScriptProcessor

setViewport(int, int) - Method in class VolumeJ.VJRenderer

Set the viewport to a specific size.

setVolume(Volume) - Method in class VJiso.VJIsosurfaceRender

The volume has changed.

setVolume(Volume) - Method in class VolumeJ.VJIsosurfaceRender

The volume has changed.

setVolume(Volume) - Method in class VolumeJ.VJRenderer

The volume has changed.

setWidth(int) - Method in class retina.OIDHeader

setWidth(int) - Method in class SpeHeader

setWidth(double) - Method in class VolumeJ.VJClassifierLevoy

Set width of gradient tent function.

setx(int) - Method in class VolumeJ.VJVoxelLoc

Set the value for x.

sety(int) - Method in class VolumeJ.VJVoxelLoc

Set the value for x.

setz(float) - Method in class VolumeJ.VJVoxelLoc

Set the value for z.

setz(int) - Method in class VolumeJ.VJVoxelLoc

Set the value for z.

shade(VJGradient) - Method in class VolumeJ.VJOutlineShader

Outline 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.VJShader

Empty shading method uses *normalized* gradient g.

shear(double, double) - Method in class VolumeJ.VJMatrix

Shear the coordinate system by sx, sy.

shortMatrixFromImageStack(ImagePlus) - Static method in class bijnum.BIJutil

Convert the data in the ImageStack in imp into a short [][] matrix for further processing.

show() - Method in class bd.BDUserInterface

show() - Method in class FlowJ.FlowJUserInterface

Shows Dialog.

showAccuracies(Features, float[], Features, float[], int, int) - Static method in class stereodisc.Analyzer

Print the accuracies for each feature used in knn search.

showAndSavePlot(float[], float[], float[], String, String, String) - Method in class scripts.ScriptProcessor

showAndSavePlots(float[][], float[][], float[], String, String, String, float[][], int) - Method in class scripts.ScriptProcessor

Show and save plots of timecourses in tc.

showDialog() - Method in class of3d.OF3DUserInterface

showDialog() - Method in class VolumeJ.VJSurfaceJ

Sets up the dialog window with all (dynamic) elements filled in.

showDialog() - Method in class VolumeJ.VJUserInterface

Sets up the dialog window with all (dynamic) elements filled in.

showGUI() - Method in class stimulator.StimulusJInterface

Sets up the dialog window with all (dynamic) elements filled in.

showGUI() - Method in class va.PVCAMInterface

Sets up the dialog window with all (dynamic) elements filled in.

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

showStatisticsPerClass(String[], float[][][], float[][], int, String) - Static method in class stereodisc.ObserverAccuracy

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

SIGMA - Static variable in class FlowJ.FlowJSpotNoise

SIGMA3DM - Static variable in class of3d.OF3DSpot

SIGMA_RELATIVE - Static variable in class volume.DoG2D

SIGMAH - Static variable in class of3d.OF3DSpot

SIGMAM - Static variable in class FlowJ.FlowJSpotNoise

sign_j(double, double) - Static method in class bijnum.Blas

This method implements the FORTRAN sign (not sin) function.

singlechannel() - Method in class VolumeJ.VJShade

size - Variable in class retina.OIDamplitudeAnalyzer

SKIPODDS - Static variable in class scripts.ScriptProcessor

Slice_Adder - Class in <Unnamed>

Adds the images in a stack as a third image, and allows the n-th image in the stack to be translated relative to the first one.

Slice_Adder() - Constructor for class Slice_Adder

sliceArray - Variable in class volume.VolumeRGB

The slices for this volume with the actual RGB data.

SlideCropper - Class in stereodisc

Slide cropper crops stereo retinal slides (macula / optic disc to a reasonable format and registers them to each other so they are aligned.

SlideCropper() - Constructor for class stereodisc.SlideCropper

slidesDirectory() - Static method in class stereodisc.Conventions

sliding(float[], int, float, int, boolean) - Static method in class volume.Equalize

Perform sliding window averaging on image.

smallest(float[], float[], int, double) - Static method in class volume.Hessian

Compute the smallest Hessian eigenvectors of a 2-D image.

smallest(float[], int, double) - Static method in class volume.Hessian

Compute the smallest Hessian eigenvectors of a 2-D image.

snr - Variable in class bijnum.BIJgifa

Sobel - Class in volume

This class implements a 2D separated Sobel differentiation kernel.

Sobel() - Constructor for class volume.Sobel

Initialize Sobel 2D kernel.

Sobel(int) - Constructor for class volume.Sobel

Sobel edge detector with edge directions around the compass.

Sobel3D - Class in volume

This class implements a 3D Sobel differentiation kernel.

Sobel3D() - Constructor for class volume.Sobel3D

Initialize Sobel 1D kernel.

SOBEL3DT - Variable in class of3d.OF3DLucas

Sobel4D - Class in volume

This class implements a 4D Sobel differentiation kernel.

Sobel4D() - Constructor for class volume.Sobel4D

Initialize Sobel 1D kernel.

sort() - Method in class bijnum.BIJJacobi

Sort the eigenvalues/eigenvectors on the basis of the eigenvalues, largest first.

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.

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() - Method in class bijnum.Jacobi

Deprecated.

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.OIDAnalysisMethods

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

SpeHeader - Class in <Unnamed>

SpeHeader() - Constructor for class SpeHeader

SpeHeader(int, int, int, int) - Constructor for class SpeHeader

SpeHeader(byte[]) - Constructor for class SpeHeader

SPEReader_ - Class in <Unnamed>

Plugin to decode and open SPE (Princeton scientific instruments) format files.

SPEReader_() - Constructor for class SPEReader_

speType(int) - Static method in class SaveAsSPE_

spot(int, int, double, int, float[]) - Method in class FlowJ.FlowJSpotNoise

spot(int, int, double, int, int, int, float[]) - Method in class FlowJ.FlowJSpotNoise

SPOTNOISE - Static variable in class FlowJ.FlowJDisplay

sqrt() - Method in class volume.VolumeFloat

sregul - Static variable in class FlowJ.FlowJLucas

SSD - Class in FlowJ

SSD(int, int) - Constructor for class FlowJ.SSD

SSD(VolumeFloat, int, int, int, int, int) - Constructor for class FlowJ.SSD

Stack_Averager - Class in <Unnamed>

Averages all images in a stack.

Stack_Averager() - Constructor for class Stack_Averager

stacksDirectory() - Static method in class stereodisc.Conventions

start - Variable in class retina.OIDProcessor

Other parameters describing the layout of aggregate.

START - Static variable in class scripts.ScriptProcessor

start() - Method in class stereo.algorithms.StopWatch

Starts the stopwatch.

start() - Method in class stimulator.StimScreen

Kick off the main loop.

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.

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

Compute stdev (SQRT(var)) of all values in vector v.

stereo - package stereo

Stereo - Class in features.filterBanks

This class implements a stereo filterbank, i.e.

Stereo(float[], int[]) - Constructor for class features.filterBanks.Stereo

Stereo(float[], float[], int[]) - Constructor for class features.filterBanks.Stereo

Stereo(float[], float[], float[], int[]) - Constructor for class features.filterBanks.Stereo

stereo.algorithms - package stereo.algorithms

StereoAnalyzer - Class in stereo

StereoAnalyzer() - Constructor for class stereo.StereoAnalyzer

StereoCostFunctions - Class in stereo

StereoCostFunctions() - Constructor for class stereo.StereoCostFunctions

stereoDifference - Static variable in class VolumeJ.VJRenderViewStereo

stereodisc - package stereodisc

StereoDoG - Class in features.filterBanks

This class implements a dog difference of gaussians filterbank, i.e.

StereoDoG(float[], float[], int[]) - Constructor for class features.filterBanks.StereoDoG

StereoPairSplitter - Class in stereo

StereoPairSplitter() - Constructor for class stereo.StereoPairSplitter

StereoPairtoJPSConverter - Class in <Unnamed>

Convert stereo image pairs to JPS format.

StereoPairtoJPSConverter() - Constructor for class StereoPairtoJPSConverter

StereoSegmentation - Class in stereo

StereoSegmentation() - Constructor for class stereo.StereoSegmentation

STIM_BARWIDTH - Static variable in class scripts.ScriptProcessor

STIM_CHECKERSIZE - Static variable in class scripts.ScriptProcessor

STIM_IDLE - Static variable in class scripts.ScriptProcessor

STIM_ISOLUMINANCE - Static variable in class scripts.ScriptProcessor

STIM_RANDOMBLOCK - Static variable in class scripts.ScriptProcessor

STIM_TYPE - Static variable in class scripts.ScriptProcessor

StimScreen - Class in stimulator

Stimulus generator package.

StimScreen() - Constructor for class stimulator.StimScreen

StimScreen(GraphicsDevice) - Constructor for class stimulator.StimScreen

Creates a new stimulus screen on a specific device.

StimScreen(GraphicsDevice, CCDcontrol) - Constructor for class stimulator.StimScreen

Creates a new stimulus screen on a specific device and for a specific camera interface.

stimulator - package stimulator

StimulusJInterface - Class in stimulator

User interface.

StimulusJInterface() - Constructor for class stimulator.StimulusJInterface

Open a new StimulusJInterface.

stop() - Method in class stereo.algorithms.StopWatch

Stops the stopwatch.

stop() - Method in class stimulator.StimScreen

StopWatch - Class in stereo.algorithms

A stopwatch accumulates time when it is running.

StopWatch() - Constructor for class stereo.algorithms.StopWatch

Constructs a stopwatch that is in the stopped state and has no time accumulated.

STRAIGHT_LINE - Static variable in class Hough_

STROBED_MODE - Static variable in class va.PVCAM

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

Subtract a matrix n from a matrix m.

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

Subtract the i'th element of a vector v from the i'th element of each column of 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

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

Subtract the j'th element of a vector v from the j'th element of each row of matrix m.

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) - 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, 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(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 m, include only those row vectors with an index which is in indices.

subset(int[]) - Method in class features.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 retina.OIDAnalysisMethods

SUBTRACT - Static variable in class retina.OIDProcessor

subtract(float[], float[]) - Static method in class volume.Convolver

Deprecated.

Subtract_Mean_Pixel - Class in <Unnamed>

This plugin subtracts the mean intensity of each pixel, to equalize the pixels over time.

Subtract_Mean_Pixel() - Constructor for class Subtract_Mean_Pixel

subtractAverage() - Method in class of3d.OF3DFlow

suggestCineViewport(Volume, VJMatrix, double, double, double, 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(float[], float[], int) - Static method in class bijnum.BIJmulticlass

sum(1) computes summation of values in vector v for class c.

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.

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

Compute average of all values in vector v.

support() - Method in class volume.Kernel

surface(VJVoxelLoc) - Method in class VJiso.VJBinaryShell

Determine whether there is a surface in the cell that vl is in.

surface(VJCell) - Method in class VJiso.VJBinaryShell

Determine whether cell contains a surface.

surface(int, int, int) - Method in class VJiso.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.

surface(VJCell) - Method in class VolumeJ.VJBinaryShell

Determine whether cell contains a surface.

surface(int, int, int) - Method in class VolumeJ.VJBinaryShell

Determine whether cell contains a surface.

SurfaceJ_ - Class in <Unnamed>

This class interfaces the VolumeJ package to a ImageJ plugin.

SurfaceJ_() - Constructor for class SurfaceJ_

SVDC - Class in bijnum

This class contains the LINPACK DSVDC (singular value decomposition) routine.

SVDC() - Constructor for class bijnum.SVDC

SVDCException - Exception in bijnum

This is the exception produced by the Singular Value Decomposition method.

SVDCException(int) - Constructor for exception bijnum.SVDCException

SVDCException(String) - Constructor for exception bijnum.SVDCException

SVDCException() - Constructor for exception bijnum.SVDCException

swapQuadrants(ImageProcessor) - Method in class Find_Disk

Swap quadrants 1 and 3 and quadrants 2 and 4 so the power spectrum origin is at the center of the image.

sweeps() - Method in class bijnum.BIJJacobi

sweeps() - Method in class bijnum.Jacobi

Deprecated.