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

S

Sample() - Method in class ij3d.ext.Imod

Description of the Method

scalarProduct(Vector3D) - Method in class ij3d.geom.Vector3D

scalar product between two vectors

segImage - Variable in class ij3d.geom.Object3D

The image where the object lies

Segment3D - Class in ij3d.image3d

Description of the Class

Segment3D(ImagePlus, int, int) - Constructor for class ij3d.image3d.Segment3D

Constructor for the Segment3D object

segmentSpot(int, int, int, int, int, IntImage3D) - Method in class ij3d.geom.Object3D

Segment an object from a seed

segmentSpotMax(int, int, int, int, int, IntImage3D) - Method in class ij3d.geom.Object3D

Segment an object from a seed, keep only max local

selection - Variable in class ij3d.align.Align2D

Description of the Field

separateWatershed() - Method in class ij3d.image3d.IntImage3D

Separate objects from an EDM image

separeSpot2D(IntImage3D, int, int, Object3D, Object3D, Object3D, double, int, int) - Method in class ij3d.geom.Object3D

serie - Variable in class ij3d.align.Align2D

Description of the Field

set(int, int, double) - Method in class ij3d.Jama.Matrix

Set a single element.

setAddAngles(float) - Method in class ij3d.ext.ImodConf

Sets the addAngles attribute of the ImodConf object

setAngleDebut(float) - Method in class ij3d.ext.ImodConf

Sets the angleDebut attribute of the ImodConf object

setAngleDebut(float) - Method in class ij3d.ext.XmippConf

Sets the angleDebut attribute of the XmippConf object

setAngleFin(float) - Method in class ij3d.ext.XmippConf

Sets the angleFin attribute of the XmippConf object

setAngleIncrement(float) - Method in class ij3d.ext.ImodConf

Sets the angleIncrement attribute of the ImodConf object

setAngleIncrement(float) - Method in class ij3d.ext.XmippConf

Sets the angleIncrement attribute of the XmippConf object

setBille(int) - Method in class ij3d.ext.ImodConf

Sets the bille attribute of the ImodConf object

setCalibration(Calibration) - Method in class ij3d.geom.Object3D

Sets the calibration attribute of the Object3D object

setCalibration(Calibration) - Method in class ij3d.geom.ObjectCreator3D

Sets the calibration attribute of the Object3D object

setCenter(boolean) - Method in class ij3d.image3d.FHTImage3D

Sets the center attribute of the FHTImage3D object

setColor(IntImage3D, String) - Method in class ij3d.image3d.ColorImage3D

met une couleur donnee a l'image3D

setColor(ImageStack, String) - Method in class ij3d.image3d.ColorImage3D

met une couleur donnee a l'image3D

setConf(ImodConf) - Method in class ij3d.ext.Imod

Sets the conf attribute of the Imod object

setConf(XmippConf) - Method in class ij3d.ext.Xmipp

Sets the conf attribute of the Xmipp object

setCoord(double, double, double) - Method in class ij3d.geom.Vector3D

Sets the attributes of the Vector3D object

setEraser(boolean) - Method in class ij3d.ext.ImodConf

Sets the eraser attribute of the ImodConf object

setExclure(String) - Method in class ij3d.ext.ImodConf

Sets the exclure attribute of the ImodConf object

setIteration(int) - Method in class ij3d.ext.XmippConf

Sets the iteration attribute of the XmippConf object

setMatrix(int, int, int, int, Matrix) - Method in class ij3d.Jama.Matrix

Set a submatrix.

setMatrix(int[], int[], Matrix) - Method in class ij3d.Jama.Matrix

Set a submatrix.

setMatrix(int[], int, int, Matrix) - Method in class ij3d.Jama.Matrix

Set a submatrix.

setMatrix(int, int, int[], Matrix) - Method in class ij3d.Jama.Matrix

Set a submatrix.

setNomSerie(String) - Method in class ij3d.ext.ImodConf

Sets the nomSerie attribute of the ImodConf object

setNomSerie(String) - Method in class ij3d.ext.XmippConf

Sets the nomSerie attribute of the XmippConf object

setPix(int, int, int, double) - Method in class ij3d.image3d.Image3D

Sets the pix attribute of the Image3D object

setPix(int, int, int, double) - Method in class ij3d.image3d.IntImage3D

Sets the pix attribute of the IntImage3D object

setPix(int, int, int, double) - Method in class ij3d.image3d.RealImage3D

Sets the pixel value at position (x,y,z) as a double

setPixel(int, int, int, float) - Method in class ij3d.geom.ColorPoint3D

Sets the pixel attribute of the Pixel3D object

setPixel(int, int, int, double) - Method in class ij3d.geom.ColorPoint3D

Sets the pixel attribute of the Pixel3D object

setPixel(int, int, int, float) - Method in class ij3d.geom.Pixel3D

Sets the pixel attribute of the Pixel3D object

setPixel(int, int, int, double) - Method in class ij3d.geom.Pixel3D

Sets the pixel attribute of the Pixel3D object

setRec(int) - Method in class ij3d.ext.XmippConf

Sets the rec attribute of the XmippConf object

setRepertoireScripts(String) - Method in class ij3d.ext.Imod

Sets the repertoireScripts attribute of the ImodConf object

setRepertoireTmp(String) - Method in class ij3d.ext.Imod

Sets the repertoireTmp attribute of the ImodConf object

setResolution(double, double, String) - Method in class ij3d.geom.Object3D

Sets the resolution attribute of the ObjectCreator3D object

setResolution(double, double, String) - Method in class ij3d.geom.ObjectCreator3D

Sets the resolution attribute of the ObjectCreator3D object

setResXY(double) - Method in class ij3d.geom.Object3D

Sets the resXY attribute of the Object3D object

setResZ(double) - Method in class ij3d.geom.Object3D

Sets the resZ attribute of the Object3D object

setRoi(Roi) - Method in class ij3d.align.Align2D

Sets the roi attribute of the Align2D object

setRotation(int, double) - Method in class ij3d.align.Align2D

Sets the rotation attribute of the Align2D object

setRotation(double, double, double) - Method in class ij3d.geom.GeomTransform3D

Sets the rotation attribute of the Transform3D object

setRotation(Vector3D, double) - Method in class ij3d.geom.GeomTransform3D

setRotationDegrees(double, double, double) - Method in class ij3d.geom.GeomTransform3D

Sets the rotation attribute of the Transform3D object

setRotationXAxis(double) - Method in class ij3d.geom.GeomTransform3D

Sets the rotation on the X Axis for the Transform

setRotationYAxis(double) - Method in class ij3d.geom.GeomTransform3D

Sets the rotation on the Y Axis for the Transform

setRotationZAxis(double) - Method in class ij3d.geom.GeomTransform3D

Sets the rotationZAxis attribute of the Transform3D object

setShiftY(float) - Method in class ij3d.ext.ImodConf

Sets the shiftY attribute of the ImodConf object

setSize(int) - Method in class ij3d.utils.TabUtil

impose une nouvelle taille au tableau

setSizes(int, int, int) - Method in class ij3d.image3d.RealImage3D

Sets the sizes attribute of the RealImage3D object

setStack(ImageStack) - Method in class ij3d.align.Align2D

Sets the images to work with

setTailleX(int) - Method in class ij3d.ext.XmippConf

Sets the tailleX attribute of the XmippConf object

setTailleY(int) - Method in class ij3d.ext.XmippConf

Sets the tailleY attribute of the XmippConf object

setThickness(int) - Method in class ij3d.ext.ImodConf

Sets the thickness attribute of the ImodConf object

setTiltAngle(float) - Method in class ij3d.ext.ImodConf

Sets the tiltAngle attribute of the ImodConf object

setTiltAxis(float) - Method in class ij3d.ext.XmippConf

Sets the tiltAxis attribute of the XmippConf object

setTransform(double, double, double, double, double, double) - Method in class ij3d.geom.GeomTransform3D

Sets the transform attribute of the GeomTransform3D object

setTranslation(int, int, int) - Method in class ij3d.align.Align2D

Sets the translation attribute of the Align2D object

setTranslation(double, double, double) - Method in class ij3d.geom.GeomTransform3D

Sets the translation attribute of the Transform

setTx(int, int) - Method in class ij3d.align.Align2D

Gets the translation on X Axis for an image

setTy(int, int) - Method in class ij3d.align.Align2D

Gets the translation on Y Axis for an image

setUnits(String) - Method in class ij3d.geom.Object3D

Sets the units attribute of the Object3D object

setValue(int) - Method in class ij3d.geom.Object3D

Sets the value attribute of the Object3D object

setX(double) - Method in class ij3d.geom.Point3D

Set the value of x

setY(double) - Method in class ij3d.geom.Point3D

Set the value of y

setZ(double) - Method in class ij3d.geom.Point3D

Set the value of z

Shell - Class in ij3d.utils

Interface avec le shell (lancement de commandes)

Shell() - Constructor for class ij3d.utils.Shell

SHORT - Static variable in class ij3d.image3d.Image3D

Description of the Field

show - Variable in class ij3d.align.Align2D

Description of the Field

showInIJ(boolean) - Method in class ij3d.align.Align2D

shows progress of computing in the status bar of ImageJ

sigma(int, double) - Method in class ij3d.align.Align2D

Description of the Method

sigma - Variable in class ij3d.geom.Object3D

sigma - Variable in class ij3d.image3d.Image3D

Description of the Field

SingularValueDecomposition - Class in ij3d.Jama

Singular Value Decomposition.

SingularValueDecomposition(Matrix) - Constructor for class ij3d.Jama.SingularValueDecomposition

Construct the singular value decomposition

sizex - Variable in class ij3d.align.Align2D

Description of the Field

sizex - Variable in class ij3d.image3d.ColorImage3D

Description of the Field

sizex - Variable in class ij3d.image3d.Image3D

Description of the Field

sizey - Variable in class ij3d.align.Align2D

Description of the Field

sizey - Variable in class ij3d.image3d.ColorImage3D

Description of the Field

sizey - Variable in class ij3d.image3d.Image3D

Description of the Field

sizez - Variable in class ij3d.align.Align2D

Description of the Field

sizez - Variable in class ij3d.image3d.ColorImage3D

Description of the Field

sizez - Variable in class ij3d.image3d.Image3D

Description of the Field

snr3D() - Method in class ij3d.image3d.ColorImage3D

Description of the Method

snr3D() - Method in class ij3d.image3d.IntImage3D

Description of the Method

sobelFilter() - Method in class ij3d.image3d.IntImage3D

Sobel-like filtering in 3D

solve(Matrix) - Method in class ij3d.Jama.CholeskyDecomposition

Solve A*X = B

solve(Matrix) - Method in class ij3d.Jama.LUDecomposition

Solve A*X = B

solve(Matrix) - Method in class ij3d.Jama.Matrix

Solve A*X = B

solve(Matrix) - Method in class ij3d.Jama.QRDecomposition

Least squares solution of A*X = B

solveTranspose(Matrix) - Method in class ij3d.Jama.Matrix

Solve X*A = B, which is also A'*X' = B'

sort() - Method in class ij3d.utils.TabUtil

trie le tableau selon l'algorithme Shell-Meitzner

sortIndex() - Method in class ij3d.utils.TabUtil

trie le tableau selon l'algorithme Shell-Meitzner

Sphere3D - Class in ij3d.geom

Class Sphere3D Simple class to define a sphere in 3D space

Sphere3D() - Constructor for class ij3d.geom.Sphere3D

Constructor for the Sphere3D object

Sphere3D(double, double, double) - Constructor for class ij3d.geom.Sphere3D

Constructor for the Sphere3D object

Sphere3D(Vector3D) - Constructor for class ij3d.geom.Sphere3D

Constructor for the Sphere3D object

split(int, int, int) - Method in class ij3d.image3d.Image3D

Split a image into sub images

stack - Variable in class ij3d.image3d.Image3D

Description of the Field

StackFolderOpener - Class in ij3d.utils

Opens a folder of images as a stack.

StackFolderOpener() - Constructor for class ij3d.utils.StackFolderOpener

start() - Method in class ij3d.utils.Chrono

Description of the Method

stop() - Method in class ij3d.utils.Chrono

Description of the Method

svd() - Method in class ij3d.Jama.Matrix

Singular Value Decomposition

swapQuadrants() - Method in class ij3d.image3d.FHTImage3D

Description of the Method

sxx - Variable in class ij3d.geom.Object3D

Centred Moments

sxy - Variable in class ij3d.geom.Object3D

Centred Moments

sxz - Variable in class ij3d.geom.Object3D

Centred Moments

syy - Variable in class ij3d.geom.Object3D

Centred Moments

syz - Variable in class ij3d.geom.Object3D

Centred Moments

szz - Variable in class ij3d.geom.Object3D

Centred Moments