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 _

C

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

Canny - Class in features.filterBanks

This class implements a filterbank for computing hessian eigenvalues at different scales.

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

CCDcontrol - Class in stimulator

Stimulus generator package.

CCDcontrol() - Constructor for class stimulator.CCDcontrol

CCS_CLEAR - Static variable in class va.PVCAM

CCS_CLEAR_CLOSE_SHTR - Static variable in class va.PVCAM

CCS_CLEAR_OPEN_SHTR - Static variable in class va.PVCAM

CCS_HALT - Static variable in class va.PVCAM

CCS_HALT_CLOSE_SHTR - Static variable in class va.PVCAM

CCS_NO_CHANGE - Static variable in class va.PVCAM

CCS_OPEN_SHTR - Static variable in class va.PVCAM

CDRStatistics - Class in stereodisc

Determine linear CDR of all observation stacks in a directory.

CDRStatistics() - Constructor for class stereodisc.CDRStatistics

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

centerVolume(Volume, VJMatrix) - Method in class VolumeJ.VJViewspaceUtil

Determine the center of volume v in coordinate system m.

CentralDiff - Class in volume

This class implements a four point central difference gradient kernel.

CentralDiff() - Constructor for class volume.CentralDiff

CGOLD - Static variable in class bijnum.BIJfit

chance - Static variable in class FlowJ.Flow3JColorNoiseMapper

chance - Static variable in class FlowJ.FlowJColorNoiseMapper

chance - Static variable in class FlowJ.FlowJSpotNoiseMapper

Channel - Class in features.color

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

channels() - Method in class VolumeJ.VJShade

check(double[][]) - Method in class bijnum.Jacobi

Deprecated.

check(int, int, int[], float) - Method in class FlowJ.SSD

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.

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

Check whether JI is really the inverse of J.

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

CIRC_NO_OVERWRITE - Static variable in class va.PVCAM

CIRC_NONE - Static variable in class va.PVCAM

CIRC_OVERWRITE - Static variable in class va.PVCAM

CIRCLE - Static variable in class Hough_

circleTransform(float[], int, double) - Method in class registration.HoughTransform

Hough transform the image for a circle with radius.

CLASS0 - Static variable in class va.PVCAM

CLASS1 - Static variable in class va.PVCAM

CLASS2 - Static variable in class va.PVCAM

CLASS3 - Static variable in class va.PVCAM

CLASS4 - Static variable in class va.PVCAM

CLASS5 - Static variable in class va.PVCAM

CLASS6 - Static variable in class va.PVCAM

classes - Static variable in class VolumeJ.VJClassifiers

classificationName - Static variable in class stereodisc.Conventions

classifier - package classifier

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.

CLEAR_PRE_EXPOSURE - Static variable in class va.PVCAM

Class 2: Clearing mode flags

clipboard(PrintWriter) - Method in class FlowJ.FlowJError

close() - Method in class Align_Stereo

Closes this window.

close() - Method in class Cropper_Scaler

Closes this window.

clsDirectory() - Static method in class stereodisc.Conventions

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

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].

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

Compute complex cell output from left and right images for phase phil/r, spatial frequency w and width s.

compose(VJAlphaColor, float) - Method in class VolumeJ.VJAlphaColor

Additive color mixing.

compose(VJAlphaColor, VJShade, float) - Method in class VolumeJ.VJAlphaColor

Additive shading and color mixing.

compute() - Method in class bd.BDColorSeparator

compute() - Method in class bd.BDVarDetector

compute() - Method in class bd.BlobDetector

compute(float[]) - Method in class bijnum.BIJfft

Compute the 1-D Fast fourier transform for x.

compute(float[], boolean) - Method in class bijnum.BIJfht

Perform a Fast Hartley Transform on an image BIJfht of maxN x maxN pixels.

compute(float[][], int) - Method in class bijnum.BIJgifa

Compute GIFA for k conditions.

compute() - Method in class bijnum.BIJJacobi

Compute all eigenvalues and eigenvectors of a real symmetric matrix a[N][N].

compute(float[][]) - Method in class bijnum.BIJpca

Compute the PCA.

compute(float[][]) - Method in class bijnum.Jacobi

Deprecated.

compute(double[][]) - Method in class bijnum.Jacobi

Deprecated.

compute(int, int[], int[], int) - Static method in class features.FeatureComputer

Compute a feature given featurenumber.

compute(float[], int) - Method in class segmentation.NormalizedOptimalConvexRegion

compute(float[], float[], int) - Method in class segmentation.NormalizedOptimalConvexRegion

compute(float[], int) - Method in class segmentation.OptimalAdmissibleRegion

Compute optimized admissible region using only regional cost.

compute(float[], float[], int) - Method in class segmentation.OptimalAdmissibleRegion

Compute optimized admissible region using regional cost as well as edge-based costs.

compute(float[], float[], int, int, int, int) - Static method in class segmentation.OptimalClosedDualPath

compute(float[], int, int) - Static method in class segmentation.OptimalClosedPath

compute(float[], int, int, OptimalClosedPath.Bounds) - Static method in class segmentation.OptimalClosedPath

compute(float[], int) - Method in class segmentation.OptimalConvexRegion

compute(float[], float[], int) - Method in class segmentation.OptimalConvexRegion

compute(float[], float[], float[], int) - Static method in class stereo.algorithms.Cyclopian

Computes the cyclopian image as a combination of two images.

compute(float[], float[], int, float, Point2D.Float, float[], int) - Static method in class stereo.algorithms.Cyclopian

Computes the cyclopian image between two images that are in polar coordinates.

compute() - Method in class volume.Diffusion

compute(float) - Method in class VolumeJ.VJShade

Compute the value of contribution after shading with this shade.

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

computeCupCost(float[], float[], int) - Static method in class stereo.StereoCostFunctions

Computes a cost function for the cup of an optic nerve.

computed - Variable in class of3d.OF3DFlow

computeFull(FlowJFlow, float, float) - Method in class FlowJ.FlowJFleet

Compute all full velocities from 5*5 neighbourhoods of normal velocities.

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, int, float) - Method in class FlowJ.FlowJUras

computeLinearCombination() - Method in class bijnum.BIJpca

Compute the linear combination of all eigenimages.

computeLinearCombination(float[]) - Method in class bijnum.BIJpca

Compute a (compacted) linear combination of the imagevectors, using only with factor set to 1.

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

computeRimCost(float[], float[], int) - Static method in class stereo.StereoCostFunctions

Computes a cost function for the rim of an optic nerve.

computeRimCost(float[], float[], Point2D.Float[], int) - Static method in class stereo.StereoCostFunctions

Computes a cost function for the rim of an optic nerve.

computeRimCost(float[], int) - Static method in class stereo.StereoCostFunctions

Computes a cost function for the rim of an optic nerve.

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

computeSegmentation(String[], Point2D.Float[], String, boolean) - Static method in class stereo.StereoSegmentation

computeSingleFrame(int) - Method in class FlowJ.FlowJUserInterface

Compute the flow from the current stack.

computeVarDeriv() - Method in class bd.BDVarDetector

computeWithDualPath(float[], float[], Point2D.Float, Point2D.Float[], int) - Static method in class stereo.StereoSegmentation

computeWithSinglePath(float[], float[], Point2D.Float, Point2D.Float[], int) - Static method in class stereo.StereoSegmentation

Compute the Rim/Cup segmentation of an image, given the a priori classification.

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

Concatenate a vector to another vector in the same order.

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

Condition analysis of timecourse data.

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

Do condition difference analysis on the average of all stimulus frames in condition 0 and 1.

CONFIDENCELIMIT - Static variable in class scripts.ScriptProcessor

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

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

CONTRAST - Static variable in class retina.OIDAnalysisMethods

CONTRAST - Static variable in class retina.OIDProcessor

ContrastNorm_Ruggeri - Class in <Unnamed>

ContrastNorm_Ruggeri() - Constructor for class ContrastNorm_Ruggeri

ContrastNormRuggeri - Class in <Unnamed>

Conventions - Class in stereodisc

Class with defaults and conventions for stereo disk file size, names, directories, etc.

Conventions() - Constructor for class stereodisc.Conventions

convert(int, int[]) - Static method in class features.color.Channel

convert(int[], int) - Static method in class features.color.HSB

convert(int[], int) - Static method in class features.color.Opponency

convert(int[], int) - Static method in class features.color.RGB

convertImageToResult(ColorProcessor, int) - Static method in class stereodisc.Conventions

Convert a ColorProcessor with an image containing different colors for different classes into an array with 0...number of classes for each pixel.

convertParametersIntoTransformationMatrix(float[], float, float) - Static method in class volume.Transformer

Convert a bunch of float 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(double[]) - Static method in class volume.Transformer

Convert a bunch of double transformation parameters into a transformation matrix.

Convolver - Class in volume

This class implements convolution operations on image planes and volumes.

Convolver() - Constructor for class volume.Convolver

convolvet(Kernel1D) - Method in class volume.HyperVolume

Compute separated 1d convolution: hv=hv1*kernel in t dimension in place.

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.

convolvex(float[], int, int, Kernel1D) - Static method in class volume.Convolver

Convolution of plane with 1D separated kernel along the x-axis.

convolvex(float[], int, int, int, Kernel1D) - Static method in class volume.Convolver

Convolution of float volume with symmetric 1D kernel in x dimension.

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(short[], 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

convolvexyz(float[], int, int, int, Kernel3D) - Static method in class volume.Convolver

Convolution of float volume with symmetric 3D kernel in all dimensions.

convolvexyz(short[], int, int, int, Kernel3D) - Static method in class volume.Convolver

Convolution of short volume with symmetric 3D kernel in all dimensions.

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(Kernel1D) - Method in class volume.VolumeFloat

XYZ convolution with separated 1D kernel.

convolvexyz(Kernel1D) - Method in class volume.VolumeShort

XYZ convolution with separated 1D kernel.

convolvey(float[], int, int, Kernel1D) - Static method in class volume.Convolver

Convolution of plane with 1D separated kernel along the y-axis.

convolvey(float[], int, int, int, Kernel1D) - Static method in class volume.Convolver

Convolution of float volume with symmetric 1D kernel in y dimension.

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, Kernel1D) - Method in class volume.VolumeFloat

convolvez(VolumeFloat) - Method in class volume.VolumeFloat

convolvez(VolumeFloat, Kernel2D) - Method in class volume.VolumeFloat

convolvez(VolumeFloat, Kernel3D) - Method in class volume.VolumeFloat

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

Copy a vector.

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

Copy a matrix.

copy(short[]) - Static method in class bijnum.BIJShortMatrix

Copy a vector.

copy(VolumeFloat) - Method in class volume.VolumeFloat

copy(VJAlphaColor) - Method in class VolumeJ.VJAlphaColor

Make a copy of this VJAlphaColor.

CorrectiveFilters - Class in features

CorrectiveFilters() - Constructor for class features.CorrectiveFilters

correctPlane(byte[], byte[]) - Method in class ImageBlender_

Correct a plane by making pixels in both of them their average mean and variance.

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

Compute the correlation of a vector with another vector b.

Correlator - Class in registration

This class implements static methods for cross-correlating images.

Correlator() - Constructor for class registration.Correlator

count() - Method in class bd.BlobDetector

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

Compute count of all occurences of class c in v.

countCupAndRimPixels(float[]) - Static method in class stereo.StereoAnalyzer

Function to count the number of cup pixels and the number of rim pixels in the image.

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

Compute the covariance matrix for a matrix of size NxM.

createCameraRepeatReferenceStandard(String[]) - Static method in class stereodisc.GroundTruthConverter

Use the order in the basenames to aggregate individual observations.

createCircularMask(int, float) - Static method in class stereo.algorithms.RankFilter

createConventionalReferenceStandard(String[]) - Static method in class stereodisc.GroundTruthConverter

Creates conventional reference standards with either aggregated over observers or for each observer.

createImage(byte[], int) - Method in class stimulator.StimScreen

Create a full screen Image from an array of pixels for display on this device.

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

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

createShape(String) - Method in class Moving_2D_Shapes

createShape(String) - Method in class Moving_3D_Shape

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 stereodisc.SlideCropper

cropLx - Static variable in class stereodisc.SlideCropper

cropLy - Static variable in class stereodisc.SlideCropper

Cropper_Scaler - Class in <Unnamed>

This plugin crops the image to a set size centered around the centroid of the current ROI, scales it by a set size and saves it under the original name.

Cropper_Scaler() - Constructor for class Cropper_Scaler

cropRx - Static variable in class stereodisc.SlideCropper

cropRy - Static variable in class stereodisc.SlideCropper

cropWidth - Static variable in class stereodisc.SlideCropper

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.

cupColor - Static variable in class stereo.StereoSegmentation

CupCost - Static variable in class stereo.StereoSegmentation

CupFeatures - Static variable in class stereo.StereoCostFunctions

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.

Cycle - Class in stimulator

Stimulus generator package.

Cycle() - Constructor for class stimulator.Cycle

Cycle(StimScreen, ByteProcessor, ByteProcessor, ByteProcessor[], int, double, double, double, double, double) - Constructor for class stimulator.Cycle

Set up an epoch.

cycles - Variable in class registration.SearchMI

Cyclopian - Class in stereo.algorithms

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