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 _

R

R - Static variable in class features.color.Channel

R(float[], int, int, double, boolean) - Method in class features.filterBanks.RadialGaussianDerivative

Compute a radial L filter of order, scale and orientation.

r - Variable in class VolumeJ.VJAlphaColor

r - Variable in class VolumeJ.VJrgbValue

RadialGaussianDerivative - Class in features.filterBanks

This class implements a filterbank for radially oriented GaussianDerivative Oriented Filter.

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

radius - Static variable in class Hough_Circle

radius - Static variable in class stereo.StereoPairSplitter

radius - Static variable in class stereo.StereoSegmentation

rampStack() - Method in class Moving_3D_Shape

random - Variable in class of3d.FlowJValue

random - Static variable in class stereo.StereoAnalyzer

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

Randomly sample a fraction of the elements of vector v.

RankFilter - Class in stereo.algorithms

A class to perform radial rank filtering.

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

RAW_OFFSET - Static variable in class retina.OIDHeader

RAW_OFFSET - Static variable in class SpeHeader

rays - Static variable in class stereo.StereoPairSplitter

rays - Static variable in class stereo.StereoSegmentation

rb - Variable in class segmentation.OptimalClosedDualPath.Bounds

rb - Variable in class segmentation.OptimalClosedPath.Bounds

read(String) - Method in class FlowJ.FlowJFlow

Read a flow field defined in a file.

read(String) - Method in class of3d.OF3DFlow

READOUT_COMPLETE - Static variable in class va.PVCAM

READOUT_IN_PROGRESS - Static variable in class va.PVCAM

READOUT_NOT_ACTIVE - Static variable in class va.PVCAM

recompute(float) - Method in class FlowJ.SSD

Reconstructors - package Reconstructors

regImages(Registerer, ImageStack, float[][]) - Static method in class registration.RegisterImageJUtilities

Register a stack of images based on a series of ROIs to the first image in is, based on the roi images in a.

Register - Class in registration

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.Registerer

register(float[]) - Method in class registration.RegisterFFT

Register the image in a to the reference image.

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.RegisterRetina

Register the image a to the reference image.

Register_ROI - Class in <Unnamed>

This class registers a stack using cross-correlation.

Register_ROI() - Constructor for class Register_ROI

Register_ROI_MI - Class in <Unnamed>

This class registers a stack to the first image in the stack using mutual information.

Register_ROI_MI() - Constructor for class Register_ROI_MI

Register_ROI_MI_Edges - Class in <Unnamed>

This class registers a stack to the first image in the stack using edge based mutual information.

Register_ROI_MI_Edges() - Constructor for class Register_ROI_MI_Edges

Registerer - Class in registration

Top class for all registration implementations.

Registerer() - Constructor for class registration.Registerer

RegisterFFT - Class in registration

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 in registration

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.

RegisterImageJUtilities - Class in registration

This class registers a stack using cross-correlation.

RegisterImageJUtilities() - Constructor for class registration.RegisterImageJUtilities

RegisterMI - Class in registration

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 in registration

Retina registration methods.

RegisterRetina(float[], int, float[]) - Constructor for class registration.RegisterRetina

Prepare for registration including preprocessing of the reference image.

registration - package registration

removeExtension(String) - Static method in class scripts.ScriptProcessor

repaint(Graphics) - Method in class stimulator.StimScreen

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

repmat replicates a vector in tiled form.

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

repmat replicates a matrix in tiled form.

reportName - Static variable in class stereodisc.Conventions

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

Stops the watch and resets the elapsed time to 0.

reset() - Method in class stimulator.StimulusJInterface

resetVolume(VJRenderer, ImagePlus, ImagePlus, double, double, double) - Static 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.

resultsDirectory() - Static method in class stereodisc.Conventions

retina - package retina

Retina_Blobs - Class in <Unnamed>

This plugin performs sliding window equalization on a stack of retinal images.

Retina_Blobs() - Constructor for class Retina_Blobs

Retina_Equalize - Class in <Unnamed>

This plugin performs sliding window equalization on a stack of retinal images.

Retina_Equalize() - Constructor for class Retina_Equalize

Retina_Register - Class in <Unnamed>

This class registers a stack of retinal images using mutual information.

Retina_Register() - Constructor for class Retina_Register

RetinalImage - Class in retina

This class contains methods to process retinal images.

RetinalImage() - Constructor for class retina.RetinalImage

RG - Static variable in class features.color.Channel

RGB - Class in features.color

RGB() - Constructor for class features.color.RGB

RGB - Static variable in class VolumeJ.VJClassifier

Classifier can return a RGB VJAlphaColor.

RGB.Channel - Enum in features.color

RGB_AutoLevels - Class in <Unnamed>

Plugin that performs the Photoshop AutoLevel LUT transformation.

RGB_AutoLevels() - Constructor for class RGB_AutoLevels

RGBtoHSB(int, int, int) - Static method in class features.color.HSB

rho - Variable in class bijnum.BIJgifa

rimColor - Static variable in class stereo.StereoSegmentation

RimCost - Static variable in class stereo.StereoSegmentation

RimFeatures - Static variable in class stereo.StereoCostFunctions

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

Compute Root Mean Square Error of vectors a and b.

ROC - Class in stereodisc

Stereo disk photograph analysis.

ROC() - Constructor for class stereodisc.ROC

rotateInPlane(float, float) - Method in class VolumeJ.VJRenderViewInteractive

Rotate the transformation matrix by viewing plane rotation angles rotx, roty.

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

Rotate a transformation matrix around the x-axis.

rotatex(double) - Method in class VolumeJ.VJMatrix

Rotate the coordinate system around the x axis.

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

Rotate a transformation matrix around the y axis.

rotatey(double) - Method in class VolumeJ.VJMatrix

Rotate the coordinate system around the y axis.

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

Rotate a transformation matrix around the z axis.

rotatez(double) - Method in class VolumeJ.VJMatrix

Rotate the coordinate system around the z axis.

roundNearest(float[]) - Static method in class stereo.algorithms.Transform

Rounds a floating point image to the nearest whole values.

rre(float[], float[]) - Static method in class stereodisc.Conventions

Calculate relative rim error (rimn = class 1).

rsDirectory() - Static method in class stereodisc.Conventions

rsName - Static variable in class stereodisc.Conventions

RTA_Reader - Class in retina

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 in retina

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 in retina

This class implements a Talia Inc Retinal Thickness (www.talia.com) Analyzer thickness map format (.m) file reader.

RTAReader() - Constructor for class retina.RTAReader

Ruggeri_Enhance_Up - Class in <Unnamed>

Ruggeri_Enhance_Up() - Constructor for class Ruggeri_Enhance_Up

RuggeriEnhanceUp - Class in <Unnamed>

RuggeriNormalizer(ImagePlus) - Method in class ContrastNormRuggeri

run(String) - Method in class Align_Stereo

run(String) - Method in class Backprojector_

run(String) - Method in class bd.TopLevel_Blob_Detection

run(ImageProcessor) - Method in class ContrastNorm_Ruggeri

run(String) - Method in class Cropper_Scaler

run(String) - Method in class Depth_Coded_Stack_

run(ImageProcessor) - Method in class Diffusion_

run(ImageProcessor) - Method in class Diffusion_4D

run(ImageProcessor) - Method in class Find_Disk

run(ImageProcessor) - Method in class Find_FOV

run(String) - Method in class FlowJ_

run(ImageProcessor) - Method in class Frequency_finder

run(ImageProcessor) - Method in class GoldFinger_

run(ImageProcessor) - Method in class Grid_maker

run(ImageProcessor) - Method in class Horiz_Correlator

run(ImageProcessor) - Method in class Hough_

run(ImageProcessor) - Method in class Hough_Circle

run(ImageProcessor) - Method in class Hough_Largest_Circle

run(String) - Method in class HTTP_

run(ImageProcessor) - Method in class ImageBlender_

run(ImageProcessor) - Method in class Map_MI

run(ImageProcessor) - Method in class Map_Timecourse

run(ImageProcessor) - Method in class MI_

run(String) - Method in class Montage_Adjusted

run(ImageProcessor) - Method in class Montage_Cutter

run(ImageProcessor) - Method in class MontageCutter_II

run(ImageProcessor) - Method in class MontageCutter_III

run(String) - Method in class Moving_2D_Shapes

run(String) - Method in class Moving_3D_Shape

run(String) - Method in class Observations_Opener

run(String) - Method in class OCT_Reader

run() - Method in class of3d.OF3DLucas

run(String) - Method in class OIDOpener_URL

run(String) - Method in class OIDReader_

run(String) - Method in class Optic_Flow_3D

run(ImageProcessor) - Method in class PCA_

run(ImageProcessor) - Method in class PCA_masked

run(ImageProcessor) - Method in class Peak_Finder

run(String) - Method in class PGM_Writer

run(String) - Method in class PVCAM_Test

run(String) - Method in class Reconstructors.Hypervolume_Shuffler

run(String) - Method in class Reconstructors.Volume_Deformer

run(ImageProcessor) - Method in class Register_ROI

run(ImageProcessor) - Method in class Register_ROI_MI

run(ImageProcessor) - Method in class Register_ROI_MI_Edges

run(ImageProcessor) - Method in class registration.RegisterImageJUtilities

run() - Method in class retina.OIDStackWindow

run() - Method in class retina.OIDWindow

run(String) - Method in class retina.RTA_Reader

run(String) - Method in class retina.RTA_Thickness_Reader

run(ImageProcessor) - Method in class Retina_Blobs

run(ImageProcessor) - Method in class Retina_Equalize

run(ImageProcessor) - Method in class Retina_Register

run(String) - Method in class RGB_AutoLevels

run(ImageProcessor) - Method in class Ruggeri_Enhance_Up

run(String) - Method in class SaveAsSPE_

RUN - Static variable in class scripts.ScriptProcessor

run(String) - Method in class Slice_Adder

run(String) - Method in class SPEReader_

run(String) - Method in class Stack_Averager

run() - Method in class stimulator.StimScreen

run(ImageProcessor) - Method in class Subtract_Mean_Pixel

run(String) - Method in class SurfaceJ_

run(ImageProcessor) - Method in class Test_

run(String) - Method in class USBCam_test

run(String) - Method in class VA_IMAQ_Test

Begin acquiring an image.

run(String) - Method in class Video_Angiography

run() - Method in class VJiso.VJIsosurfaceRender

Variables are all inherited from VJRenderer

run(String) - Method in class Volume_Reconstructor_

run() - Method in class VolumeJ.VJIsosurfaceRender

Variables are all inherited from VJRenderer

run() - Method in class VolumeJ.VJRender

Objectspace rendering method.

run() - Method in class VolumeJ.VJRenderer

To be overloaded, does nothing.

run() - Method in class VolumeJ.VJRenderView

Overload to make functional.

run() - Method in class VolumeJ.VJRenderViewCine

The top level rendering thread handler.

run() - Method in class VolumeJ.VJRenderViewInteractive

Generates the first view and stays on.

run() - Method in class VolumeJ.VJRenderViewSingle

The top level rendering thread handler.

run() - Method in class VolumeJ.VJRenderViewStereo

run() - Method in class VolumeJ.VJViewspaceRender

Viewspace rendering.

run(String) - Method in class VolumeJ_

run(int, int, int, int, int, int, double, double, double, double, double, double, double, int, int, int, double, double, String, int, int) - Method in class VolumeJ_

Interface for macro control of volume rendering.

rx - Static variable in class stereodisc.JPStoStack

rx - Static variable in class stereodisc.Nidek3DXToJPS

ry - Static variable in class stereodisc.JPStoStack

ry - Static variable in class stereodisc.Nidek3DXToJPS