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A

About - Class in mcib_plugins
 
About() - Constructor for class mcib_plugins.About
 
AboutMCIB - Class in mcib3d.utils
Description of the Class
AboutMCIB(String) - Constructor for class mcib3d.utils.AboutMCIB
Constructor for the AboutWindow object
AbstractLog - Class in mcib3d.utils.Logger
Created by thomasb on 15/11/16.
AbstractLog() - Constructor for class mcib3d.utils.Logger.AbstractLog
 
actionPerformed(ActionEvent) - Method in class mcib_plugins.ConnectionThresholding_
Description of the Method
actionPerformed(ActionEvent) - Method in class mcib_plugins.tools.ResultsFrame
 
activateAverage(int) - Method in class mcib3d.align.Align3D
Description of the Method
activateAverageAll() - Method in class mcib3d.align.Align3D
Description of the Method
ADAPTIVE - Static variable in class mcib3d.image3d.processing.FastFilters3D
 
adaptiveFilter(ImageFloat, float, float, float, int, int, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageFloat
 
adaptiveFilter(float, float, float, int) - Method in class mcib3d.image3d.ImageFloat
Deprecated.
adaptiveFilter(ImageInt, float, float, float, int, int, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageInt
 
adaptiveFilter(float, float, float, int) - Method in class mcib3d.image3d.ImageInt
Deprecated.
adaptiveFilter(float, float, float, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Adaptive Filter in 3D (expermimental) Take 7 neighborhood, compute mean and std dev Assign mean of neighborhood with lowest std dev
adaptiveFilter(float, float, float, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Adaptive Filter in 3D (expermimental) Take 7 neighborhood, compute mean and std dev Assign mean of neighborhood with lowest std dev
add(Vector3D) - Method in class mcib3d.geom.Vector3D
Add a vector
add(Vector3D, float, float) - Method in class mcib3d.geom.Vector3D
add a vector with ration
add(Vector3D, double, double) - Method in class mcib3d.geom.Vector3D
Description of the Method
add(RealImage3D) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
adds a RealImage3D to this one
add(RealImage3D, ArrayUtil) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
adds a transformed RealImage3D to this one
add(RealImage3D, GeomTransform3D) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
adds a transformed RealImage3D to this one
ADD - Static variable in class mcib3d.image3d.processing.FastArithmetic3D
 
ADD - Static variable in class mcib3d.image3d.processing.FastOperation3D
 
add(double[], Object) - Method in class mcib3d.utils.KDTreeC
Add a key and its associated value to the tree.
addAssociation(AssociationRegion) - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
addAssoRegion(AssociationRegion) - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
addAttribute(String) - Method in class mcib3d.Classification.Attributes
 
addChild(ObjectTrack) - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
addColor(IntImage3D) - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
ajoute une couleur a l'image3D si c'est possible
addColor(ImageStack) - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
ajoute une couleur a l'image3D si c'est possible
addData(Data) - Method in class mcib3d.Classification.DataSet
 
addImage(ImageInt, int, Calibration) - Method in class mcib3d.geom.Objects3DPopulation
Deprecated.
addImage(ImageHandler, int) - Method in class mcib3d.geom.Objects3DPopulation
 
addImage(ImageInt, Calibration) - Method in class mcib3d.geom.Objects3DPopulation
Deprecated.
addImage(ImagePlus) - Method in class mcib3d.geom.Objects3DPopulation
Deprecated.
addImage(ImageHandler, float, float) - Method in class mcib3d.image3d.ImageHandler
Compute the operation s1*this + s2*other
addImage(ImageHandler, int, int) - Method in class mcib3d.image3d.ImageHandler
 
addImage(ImageInt) - Method in class mcib3d.image3d.ImageInt
 
addImage(IntImage3D, float) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Adds a feature to the Image attribute of the IntImage3D object
addImage(Image3D, float, float) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Adds a feature to the Image attribute of the RealImage3D object
addImage(RealImage3D, float) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Adds a feature to the Image attribute of the RealImage3D object
addImageWithOffset(ImageHandler, int) - Method in class mcib3d.geom.Objects3DPopulation
 
addInteraction(PairColocalisation) - Method in class mcib3d.geom.interactions.InteractionsList
 
addInteraction(Object3D, Object3D) - Method in class mcib3d.geom.interactions.InteractionsList
 
addInteraction(Object3D, Object3D, int) - Method in class mcib3d.geom.interactions.InteractionsList
 
addListVoxels(LinkedList, ImagePlus) - Method in class mcib_plugins.tools.RoiManager3D_2
 
addMask(ImageInt) - Method in class mcib3d.image3d.ImageByte
 
addMe(Vector3D) - Method in class mcib3d.geom.Vector3D
Add a vector to current vector
addMe(Vector3D, double) - Method in class mcib3d.geom.Vector3D
 
addObject(Object3D) - Method in class mcib3d.geom.Objects3DPopulation
Add an object to the population
addObject3D(Object3D) - Method in class mcib_plugins.tools.RoiManager3D_2
 
addObjects(Object3D[]) - Method in class mcib3d.geom.Objects3DPopulation
 
addObjects(ArrayList<Object3D>) - Method in class mcib3d.geom.Objects3DPopulation
 
addObjects3D(Object3D[]) - Method in class mcib_plugins.tools.RoiManager3D_2
 
addObjects3D(ArrayList<Object3D>) - Method in class mcib_plugins.tools.RoiManager3D_2
 
addObjects3DPopulation(Objects3DPopulation) - Method in class mcib_plugins.tools.RoiManager3D_2
 
addPoints(Point3D[]) - Method in class mcib3d.geom.Objects3DPopulation
 
addRegion(int) - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
addRotation(int, double) - Method in class mcib3d.align.Align2D
Adds a feature to the Rotation attribute of the Align2D object
addTransform(GeomTransform3D) - Method in class mcib3d.geom.GeomTransform3D
Adds a feature to the Transform attribute of the GeomTransform3D object
addTransform(ArrayUtil) - Method in class mcib3d.geom.GeomTransform3D
Adds a feature to the Transform attribute of the GeomTransform3D object
addTranslation(int, int, int) - Method in class mcib3d.align.Align2D
Adds a feature to the Translation attribute of the Align2D object
addValue(float) - Method in class mcib3d.image3d.ImageHandler
 
addValue(int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Description of the Method
addValue(float) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
adds a given value to all pixels
addValue(int, double) - Method in class mcib3d.utils.ArrayUtil
Addition a value at a index
addValueArray(ArrayUtil) - Method in class mcib3d.utils.ArrayUtil
 
addVox(ImageLabeller.Vox3D) - Method in class mcib3d.image3d.ImageLabeller.Spot3D
 
addVox(ImageLabeller2D.Vox2D) - Method in class mcib3d.image3d.ImageLabeller2D.Spot2D
 
addVoxels(LinkedList<Voxel3D>) - Method in class mcib3d.geom.Object3DVoxels
 
addVoxelsIntersection(Object3D, Object3D) - Method in class mcib3d.geom.Object3DVoxels
 
addVoxelsIntersection(ArrayList<Object3D>) - Method in class mcib3d.geom.Object3DVoxels
 
addVoxelsUnion(Object3D, Object3D) - Method in class mcib3d.geom.Object3DVoxels
 
addVoxelsUnion(ArrayList<Object3D>) - Method in class mcib3d.geom.Object3DVoxels
 
adjustmentValueChanged(AdjustmentEvent) - Method in class mcib_plugins.ConnectionThresholding_
Description of the Method
adjustmentValueChanged(AdjustmentEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
ai - Variable in class mcib3d.utils.ThreadRunner
 
Align() - Method in class mcib3d.ext.Imod
Description of the Method
Align2() - Method in class mcib3d.ext.Imod
Description of the Method
Align2(String) - Method in class mcib3d.ext.Imod
Description of the Method
Align2D - Class in mcib3d.align
Description of the Class
Align2D(ImageStack) - Constructor for class mcib3d.align.Align2D
Constructor for the Align2D object
align2D(ImageProcessor, int, double, double) - Method in class mcib3d.align.Align2D
Description of the Method
Align3D - Class in mcib3d.align
Description of the Class
Align3D(RealImage3D[], ArrayUtil[], String) - Constructor for class mcib3d.align.Align3D
Constructor for the Align3D object
alignAllWithProjection(int, int, float, float) - Method in class mcib3d.align.Align3D
Description of the Method
alignWithProjection(int, int, int, float, float) - Method in class mcib3d.align.Align3D
Description of the Method
AllRegionsAssociation - Class in mcib3d.image3d.regionGrowing
/** Copyright (C) 2008- 2012 Thomas Boudier and others This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
AllRegionsAssociation() - Constructor for class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
angle(Object3D, Object3D) - Method in class mcib3d.geom.Object3D
Angle between (a, this, b) with real coordinates
angle(Vector3D) - Method in class mcib3d.geom.Vector3D
angle between two vectors in radians between 0 and PI
angleDegrees(Vector3D) - Method in class mcib3d.geom.Vector3D
angle between two vectors in degrees between 0 and 180
anglePlane(double, double, double, double) - Method in class mcib3d.geom.Vector3D
 
anglePlaneDegrees(double, double, double, double) - Method in class mcib3d.geom.Vector3D
 
appendMasks(Iterable<ImageInt>, int) - Method in class mcib3d.image3d.ImageShort
??
appendRotation(double, Vector3D) - Method in class mcib3d.geom.Gradient
Ajoute ensuite une transformation de type rotation à la matrice selon un axe quelconque
appendScale(double, double, double) - Method in class mcib3d.geom.Gradient
Ajout ensuite une transformation de type homothétie à la matrice
appendTranslation(double, double, double) - Method in class mcib3d.geom.Gradient
Ajoute ensuite une transformation de type translation à la matrice
applyTransform(GeomTransform3D) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
applique une transformation 3D a une image (inversion de la matrice realisee pour trouver le pixel (i,j,k) dans l'image originale)
areaContactUnit - Variable in class mcib3d.geom.Object3D
Area in units
areaContactVoxels - Variable in class mcib3d.geom.Object3D
 
areaNbVoxels - Variable in class mcib3d.geom.Object3D
Area in voxels
arrayLeftDivide(Matrix) - Method in class mcib3d.Jama.Matrix
Element-by-element left division, C = A.\B
arrayLeftDivideEquals(Matrix) - Method in class mcib3d.Jama.Matrix
Element-by-element left division in place, A = A.\B
arrayRightDivide(Matrix) - Method in class mcib3d.Jama.Matrix
Element-by-element right division, C = A./B
arrayRightDivideEquals(Matrix) - Method in class mcib3d.Jama.Matrix
Element-by-element right division in place, A = A./B
arrayTimes(Matrix) - Method in class mcib3d.Jama.Matrix
Element-by-element multiplication, C = A.*B
arrayTimesEquals(Matrix) - Method in class mcib3d.Jama.Matrix
Element-by-element multiplication in place, A = A.*B
ArrayUtil - Class in mcib3d.utils
class allowing :
storage of arrays with util function such as statistics and sorting
ArrayUtil(int) - Constructor for class mcib3d.utils.ArrayUtil
constructeur
ArrayUtil(double[]) - Constructor for class mcib3d.utils.ArrayUtil
constructeur
ArrayUtil(int[]) - Constructor for class mcib3d.utils.ArrayUtil
 
ArrayUtil(ArrayList<Double>) - Constructor for class mcib3d.utils.ArrayUtil
 
Association - Class in mcib3d.tracking_dev
 
Association(Objects3DPopulation, Objects3DPopulation, AssociationCost) - Constructor for class mcib3d.tracking_dev.Association
 
Association_ - Class in mcib_plugins
 
Association_() - Constructor for class mcib_plugins.Association_
 
Association_Track_Plugin - Class in mcib3d.tracking_dev
 
Association_Track_Plugin() - Constructor for class mcib3d.tracking_dev.Association_Track_Plugin
 
Association_Tracking - Class in mcib_plugins
 
Association_Tracking() - Constructor for class mcib_plugins.Association_Tracking
 
AssociationCost - Interface in mcib3d.tracking_dev
 
AssociationPair - Class in mcib3d.tracking_dev
 
AssociationPair(Object3D, Object3D, double) - Constructor for class mcib3d.tracking_dev.AssociationPair
 
AssociationRegion - Class in mcib3d.image3d.regionGrowing
/** Copyright (C) 2008- 2012 Thomas Boudier and others This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
AssociationRegion() - Constructor for class mcib3d.image3d.regionGrowing.AssociationRegion
 
Attributes - Class in mcib3d.Classification
 
Attributes(int) - Constructor for class mcib3d.Classification.Attributes
 
autoApplyTransform(GeomTransform3D) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
average(int) - Method in class mcib3d.align.Align2D
Description of the Method
average(boolean[]) - Method in class mcib3d.align.Align2D
average images using a selection
average() - Method in class mcib3d.align.Align3D
Description of the Method

B

b_closed(float, float, float) - Method in class mcib3d.geom.Object3D
 
b_open(float, float, float) - Method in class mcib3d.geom.Object3D
 
BACK - Static variable in class mcib_plugins.Filter3D.Kernel3D
 
bandPassFilter(float, float, float, float) - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Band Pass Filter
basicTranslation(ArrayUtil[]) - Method in class mcib3d.align.Align2D
Description of the Method
BestCriteriaMax - Class in mcib3d.image3d.IterativeThresholding
Created by thomasb on 20/4/16.
BestCriteriaMax() - Constructor for class mcib3d.image3d.IterativeThresholding.BestCriteriaMax
 
BestCriteriaMin - Class in mcib3d.image3d.IterativeThresholding
Created by thomasb on 20/4/16.
BestCriteriaMin() - Constructor for class mcib3d.image3d.IterativeThresholding.BestCriteriaMin
 
BestCriteriaStable - Class in mcib3d.image3d.IterativeThresholding
Created by thomasb on 20/4/16.
BestCriteriaStable() - Constructor for class mcib3d.image3d.IterativeThresholding.BestCriteriaStable
 
BestCriterion - Interface in mcib3d.image3d.IterativeThresholding
Created by thomasb on 20/4/16.
bigLabel - Variable in class mcib3d.image3d.Segment3DSpots
 
binarisation(double, double) - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Description of the Method
binarisation(int, int) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Thresholding, create a binarised image
binarisation(int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
binarisation de l'image, creation d'une image avec 255 si entre les deux seuils
binarisation(int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
binarisation de l'image
Binary_Close - Class in mcib_plugins
 
Binary_Close() - Constructor for class mcib_plugins.Binary_Close
 
Binary_Interpolator - Class in mcib_plugins
 
Binary_Interpolator() - Constructor for class mcib_plugins.Binary_Interpolator
 
Binary_Open - Class in mcib_plugins.processing
 
Binary_Open() - Constructor for class mcib_plugins.processing.Binary_Open
 
binaryClose(ImageInt, float, float) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryClose(ImageHandler, float, float, int) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryCloseMultilabel(ImageInt, float, float) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryCloseMultilabel(ImageInt, float, float, int) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryCloseMultilabel(ImageInt, float[], float[], int) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryDilate(ImageInt, float, float) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryDilate(ImageHandler, float, float, int, boolean) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryDilate(ImageHandler, float, float, int) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryDilate2D(ImageByte, float, boolean) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryDilateMultilabel(ImageInt, float, float) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryDilateMultilabel(ImageInt, float, float, int) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryDilateMultilabel(ImageInt, float[], float[], int) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryErode(ImageInt, float, float) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryErode(ImageHandler, float, float, int) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryErode2D(ImageByte, float) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
BinaryInterpolator - Class in mcib_plugins
 
BinaryInterpolator() - Constructor for class mcib_plugins.BinaryInterpolator
 
BinaryMorpho - Class in mcib3d.image3d.processing
* /** Copyright (C) 2012 Jean Ollion
BinaryMorpho() - Constructor for class mcib3d.image3d.processing.BinaryMorpho
 
binaryMorpho(ImageInt, int, float, float) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryMorpho(ImageHandler, int, float, float, int) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryOpen(ImageHandler, float, float) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryOpen(ImageHandler, float, float, int) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryOpenMultilabel(ImageInt, float, float) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryOpenMultilabel(ImageInt, float, float, int) - Static method in class mcib3d.image3d.processing.BinaryMorpho
 
binaryReconstruct(ImageInt) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Description of the Method
binaryReconstructByObjects(ImageInt) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
BlankMask - Class in mcib3d.image3d
/** Copyright (C) 2012 Jean Ollion This file is part of tango tango is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
BlankMask(String, int, int, int) - Constructor for class mcib3d.image3d.BlankMask
 
BlankMask(ImageHandler) - Constructor for class mcib3d.image3d.BlankMask
 
BLUE - Variable in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Description of the Field
BOTTOM - Static variable in class mcib_plugins.Filter3D.Kernel3D
 
buildObject3DVoxels() - Method in class mcib3d.geom.Object3DLabel
 
buildObject3DVoxels() - Method in class mcib3d.geom.Object3DSurface
 
bx - Variable in class mcib3d.geom.Object3D
IsoBarycenter x
by - Variable in class mcib3d.geom.Object3D
IsoBarycenter x
BYTE - Static variable in class mcib3d.image3d.legacy.Image3D
Deprecated.
BYTE
bz - Variable in class mcib3d.geom.Object3D
IsoBarycenter y

C

calculeDeriche(float) - Method in class mcib3d.geom.deformation3d.Deriche
 
calculGradient() - Method in class mcib3d.geom.deformation3d.Deriche
 
Canny_Symmetry - Class in mcib_plugins
 
Canny_Symmetry() - Constructor for class mcib_plugins.Canny_Symmetry
 
CannyDeriche1D - Class in mcib3d.image3d.processing
/** Copyright (C) 2008- 2012 Thomas Boudier and others This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
CannyDeriche1D(double[], double) - Constructor for class mcib3d.image3d.processing.CannyDeriche1D
 
CannyEdge3D - Class in mcib3d.image3d.processing
 
CannyEdge3D(ImageHandler, double) - Constructor for class mcib3d.image3d.processing.CannyEdge3D
 
canvasResized() - Method in class mcib_plugins.tools.RoiManager3D_2
 
CCF(int) - Method in class mcib3d.image3d.processing.ImageColocalizer
 
cdf(ArrayUtil) - Static method in class mcib3d.utils.CDFTools
 
cdf(ArrayUtil, ArrayUtil) - Static method in class mcib3d.utils.CDFTools
 
cdfAverage(ArrayUtil[]) - Static method in class mcib3d.utils.CDFTools
 
cdfAverage(ArrayUtil[], ArrayUtil) - Static method in class mcib3d.utils.CDFTools
 
cdfDifferences(ArrayUtil, ArrayUtil, ArrayUtil, ArrayUtil) - Static method in class mcib3d.utils.CDFTools
 
cdfPercentage(ArrayUtil[], ArrayUtil, double) - Static method in class mcib3d.utils.CDFTools
 
cdfPercentage2(ArrayUtil[], ArrayUtil, double) - Static method in class mcib3d.utils.CDFTools
 
CDFTools - Class in mcib3d.utils
 
CDFTools() - Constructor for class mcib3d.utils.CDFTools
 
center() - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Description of the Method
centerCrop(int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
centerFeatures(ArrayUtil[]) - Method in class mcib3d.align.Align2D
Description of the Method
centerInside() - Method in class mcib3d.geom.Object3D
 
centerx - Variable in class mcib3d.image3d.legacy.Image3D
Deprecated.
center x of the image
centery - Variable in class mcib3d.image3d.legacy.Image3D
Deprecated.
center y of the image
centerz - Variable in class mcib3d.image3d.legacy.Image3D
Deprecated.
center z of the image
changeImage(int, ImageProcessor) - Method in class mcib3d.align.Align2D
Description of the Method
changeStack(ImageStack) - Method in class mcib3d.align.Align2D
changes the ImageStack on which alignment is performed
CheckInstall - Class in mcib3d.utils
/** Copyright (C) 2008- 2012 Thomas Boudier and others This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
CheckInstall() - Constructor for class mcib3d.utils.CheckInstall
 
checkObjectsRelation(int, int, String) - Method in class mcib3d.geom.MereoAnalysis
 
checkValidMitosis(Object3D, Object3D, ImageHandler) - Static method in class mcib3d.tracking_dev.Mitosis
 
chol() - Method in class mcib3d.Jama.Matrix
Cholesky Decomposition
CholeskyDecomposition - Class in mcib3d.Jama
Cholesky Decomposition.
CholeskyDecomposition(Matrix) - Constructor for class mcib3d.Jama.CholeskyDecomposition
Cholesky algorithm for symmetric and positive definite matrix.
Chrono - Class in mcib3d.utils
Class that defines a chronometer
Chrono() - Constructor for class mcib3d.utils.Chrono
Constructor for the Chrono object
Chrono(int) - Constructor for class mcib3d.utils.Chrono
Constructor for the Chrono object
Classifier - Class in mcib3d.Classification
 
Classifier() - Constructor for class mcib3d.Classification.Classifier
 
classify(Data) - Method in class mcib3d.Classification.Classifier
 
CleanUpLocalThickness - Class in mcib3d.image3d.distanceMap3d
Deprecated.
CleanUpLocalThickness() - Constructor for class mcib3d.image3d.distanceMap3d.CleanUpLocalThickness
Deprecated.
 
clear() - Method in class mcib3d.geom.ObjectCreator3D
 
clone() - Method in class mcib3d.Jama.Matrix
Clone the Matrix object.
close() - Method in class mcib3d.image3d.processing.ManualSpot
 
close() - Method in class mcib_plugins.ConnectionThresholding_
Overrides close() in PlugInFrame.
CLOSEGRAY - Static variable in class mcib3d.image3d.processing.FastFilters3D
 
closeImagePlus() - Method in class mcib3d.image3d.ImageHandler
 
closestBorder(double, double, double, double) - Method in class mcib3d.geom.Objects3DPopulation
 
closestBorder(Object3D, ArrayList<Object3D>) - Method in class mcib3d.geom.Objects3DPopulation
 
closestBorder(Object3D, double) - Method in class mcib3d.geom.Objects3DPopulation
Get the closest object in the population from given object with distance greater than given distance, distance border to border between objects
closestBorder(Object3D, int[], double) - Method in class mcib3d.geom.Objects3DPopulation
 
closestBorder(Object3D) - Method in class mcib3d.geom.Objects3DPopulation
Get the closest object in the population from given object Border to border distance
closestBorder(Object3D, int[]) - Method in class mcib3d.geom.Objects3DPopulation
 
closestBorder(double, double, double) - Method in class mcib3d.geom.Objects3DPopulation
 
closestCenter(double, double, double, double) - Method in class mcib3d.geom.Objects3DPopulation
 
closestCenter(Object3D, ArrayList<Object3D>) - Method in class mcib3d.geom.Objects3DPopulation
 
closestCenter(double, double, double) - Method in class mcib3d.geom.Objects3DPopulation
 
closestCenter(Point3D) - Method in class mcib3d.geom.Objects3DPopulation
 
closestCenter(Object3D, double) - Method in class mcib3d.geom.Objects3DPopulation
Get the closest object in the population from given object with distance greater than given distance
closestCenter(Object3D, int[], double) - Method in class mcib3d.geom.Objects3DPopulation
 
closestCenter(Object3D, boolean) - Method in class mcib3d.geom.Objects3DPopulation
Get the closest object in the population from given object Center to center distance
closestCenter(Object3D, int[], boolean) - Method in class mcib3d.geom.Objects3DPopulation
 
closestsBorderK() - Method in class mcib3d.geom.ObjectsPopulationDistances
 
closestsBorderK(int) - Method in class mcib3d.geom.ObjectsPopulationDistances
 
closing() - Method in class mcib_plugins.tools.RoiManager3D_2
 
closing3D(float, float, float, int, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Fermeture binaire 3D, normalement les objets sont noir sur fond blanc
closing3D(Image3D, int, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Fermeture binaire 3D avec kernel, normalement les objets sont noir sur fond blanc
closing3D(int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Fermeture binaire 3D, normalement les objets sont noir sur fond blanc
Cluster - Class in mcib3d.image3d.regionGrowing
/** Copyright (C) 2008- 2012 Thomas Boudier and others This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
Cluster() - Constructor for class mcib3d.image3d.regionGrowing.Cluster
 
colinear(Vector3D) - Method in class mcib3d.geom.Vector3D
Computes the colinearity between two vectors that is to say the absolute value of cross product between normalized vectors
ColorImage3D - Class in mcib3d.image3d.legacy
Deprecated.
ColorImage3D() - Constructor for class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
constructeur d'un volume vide attention rien dedans maximum de couleur
ColorImage3D(int) - Constructor for class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
constructeur d'un volume vide attention rien dedans nombre de couleur fourni
ColorImage3D(int, int, int) - Constructor for class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
constructeur d'un volume vide (noir)
ColorImage3D(int, int, int, int) - Constructor for class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
constructeur d'un volume vide (noir)
comment - Variable in class mcib3d.geom.Object3D
comment on the object (not used yet)
ComparatorBorderDistance - Class in mcib3d.geom
 
ComparatorBorderDistance() - Constructor for class mcib3d.geom.ComparatorBorderDistance
 
ComparatorByte - Class in mcib3d.image3d.comparator
 
ComparatorByte(ImageByte) - Constructor for class mcib3d.image3d.comparator.ComparatorByte
 
ComparatorFloat - Class in mcib3d.image3d.comparator
 
ComparatorFloat(ImageFloat) - Constructor for class mcib3d.image3d.comparator.ComparatorFloat
 
ComparatorInvByte - Class in mcib3d.image3d.comparator
 
ComparatorInvByte(ImageByte) - Constructor for class mcib3d.image3d.comparator.ComparatorInvByte
 
ComparatorInvFloat - Class in mcib3d.image3d.comparator
 
ComparatorInvFloat(ImageFloat) - Constructor for class mcib3d.image3d.comparator.ComparatorInvFloat
 
ComparatorInvShort - Class in mcib3d.image3d.comparator
 
ComparatorInvShort(ImageShort) - Constructor for class mcib3d.image3d.comparator.ComparatorInvShort
 
ComparatorObjectTrack - Class in mcib3d.image3d.IterativeThresholding
 
ComparatorObjectTrack() - Constructor for class mcib3d.image3d.IterativeThresholding.ComparatorObjectTrack
 
ComparatorShort - Class in mcib3d.image3d.comparator
 
ComparatorShort(ImageShort) - Constructor for class mcib3d.image3d.comparator.ComparatorShort
 
ComparatorVoxel - Class in mcib3d.geom
 
ComparatorVoxel() - Constructor for class mcib3d.geom.ComparatorVoxel
 
compare(ObjectDistBB, ObjectDistBB) - Method in class mcib3d.geom.ComparatorBorderDistance
 
compare(Voxel3DComparable, Voxel3DComparable) - Method in class mcib3d.geom.ComparatorVoxel
 
compare - Variable in class mcib3d.geom.Object3D
 
compare(Object3D, Object3D) - Method in class mcib3d.geom.Object3DFactory.ObjectValueComparator
Deprecated.
 
compare(Integer, Integer) - Method in class mcib3d.image3d.comparator.ComparatorByte
 
compare(Integer, Integer) - Method in class mcib3d.image3d.comparator.ComparatorFloat
 
compare(Integer, Integer) - Method in class mcib3d.image3d.comparator.ComparatorInvByte
 
compare(Integer, Integer) - Method in class mcib3d.image3d.comparator.ComparatorInvFloat
 
compare(Integer, Integer) - Method in class mcib3d.image3d.comparator.ComparatorInvShort
 
compare(Integer, Integer) - Method in class mcib3d.image3d.comparator.ComparatorShort
 
compare(ObjectTrack, ObjectTrack) - Method in class mcib3d.image3d.IterativeThresholding.ComparatorObjectTrack
 
compareTo(Object3D) - Method in class mcib3d.geom.Object3D
 
compareTo(Voxel3D) - Method in class mcib3d.geom.Voxel3D
 
compareTo(VoxEVF) - Method in class mcib3d.image3d.distanceMap3d.VoxEVF
 
compute(ImageHandler) - Method in interface mcib3d.geom.interactions.InteractionsCompute
 
compute(ImageHandler) - Method in class mcib3d.geom.interactions.InteractionsComputeContours
 
compute(ImageHandler) - Method in class mcib3d.geom.interactions.InteractionsComputeDamLines
 
compute(ImageHandler) - Method in class mcib3d.geom.interactions.InteractionsComputeDilate
 
compute(ImageHandler) - Method in class mcib3d.geom.interactions.InteractionsComputeVoronoi
 
compute(Objects3DPopulation) - Method in class mcib3d.spatial.descriptors.F_Function
 
compute(Objects3DPopulation) - Method in class mcib3d.spatial.descriptors.G_Border
 
compute(Objects3DPopulation) - Method in class mcib3d.spatial.descriptors.G_Function
 
compute(Objects3DPopulation) - Method in class mcib3d.spatial.descriptors.H_Border
 
compute(Objects3DPopulation) - Method in class mcib3d.spatial.descriptors.H_Function
 
compute(Objects3DPopulation) - Method in class mcib3d.spatial.descriptors.K_Function
 
compute(Objects3DPopulation) - Method in interface mcib3d.spatial.descriptors.SpatialDescriptor
 
computeAllForces(boolean) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
computeAllRegionsAssociationPairs(ImageHandler, int) - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
computeAssociation - Variable in class mcib3d.image3d.regionGrowing.Watershed3D_old
 
computeAssociation() - Method in class mcib3d.tracking_dev.Association
 
computeAssociations(boolean) - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
computeBBox(ArrayList<Point3f>) - Method in class mcib3d.geom.deformation3d.Mesh
 
computeBestCriterion(ArrayUtil) - Method in class mcib3d.image3d.IterativeThresholding.BestCriteriaMax
 
computeBestCriterion(ArrayUtil) - Method in class mcib3d.image3d.IterativeThresholding.BestCriteriaMin
 
computeBestCriterion(ArrayUtil) - Method in class mcib3d.image3d.IterativeThresholding.BestCriteriaStable
 
computeBestCriterion(ArrayUtil) - Method in interface mcib3d.image3d.IterativeThresholding.BestCriterion
 
computeBounding() - Method in class mcib3d.geom.Object3D
Compute the bounding box of the object
computeBounding() - Method in class mcib3d.geom.Object3DFuzzy
 
computeBounding() - Method in class mcib3d.geom.Object3DLabel
Compute the bounding box of the object
computeBounding() - Method in class mcib3d.geom.Object3DSurface
 
computeBounding() - Method in class mcib3d.geom.Object3DVoxels
Compute the bounding box of the object
computeCenter(List<Point3f>) - Method in class mcib3d.geom.deformation3d.Mesh
 
computeCenter() - Method in class mcib3d.geom.Object3D
Compute the barycenter of the object
computeCenter() - Method in class mcib3d.geom.Object3DFuzzy
 
computeCenter() - Method in class mcib3d.geom.Object3DLabel
Compute the barycenter and the volume
computeCenter() - Method in class mcib3d.geom.Object3DSurface
 
computeCenter() - Method in class mcib3d.geom.Object3DVoxels
Compute the barycenter and the volume
computeContours(ImageHandler) - Static method in class mcib3d.geom.interactions.Interactions
 
computeContours() - Method in class mcib3d.geom.Object3D
Compute the contour voxels of the object
computeContours(ImageHandler) - Method in class mcib3d.geom.Object3D
The contours is given in an image (see OC3D)
computeContours() - Method in class mcib3d.geom.Object3DFuzzy
 
computeContours() - Method in class mcib3d.geom.Object3DLabel
 
computeContours() - Method in class mcib3d.geom.Object3DSurface
 
computeContours() - Method in class mcib3d.geom.Object3DVoxels
Compute the contours of the object rad=0.5
computeConvexHull3D() - Method in class mcib3d.geom.deformation3d.Mesh
 
computeConvexHull3D() - Method in class mcib3d.geom.Object3DSurface
 
computeCriterion(Object3D) - Method in interface mcib3d.image3d.IterativeThresholding.Criterion
 
computeCriterion(Object3D) - Method in class mcib3d.image3d.IterativeThresholding.CriterionClassification
 
computeCriterion(Object3D) - Method in class mcib3d.image3d.IterativeThresholding.CriterionCompactness
 
computeCriterion(Object3D) - Method in class mcib3d.image3d.IterativeThresholding.CriterionEdge
 
computeCriterion(Object3D) - Method in class mcib3d.image3d.IterativeThresholding.CriterionElongation
 
computeCriterion(Object3D) - Method in class mcib3d.image3d.IterativeThresholding.CriterionVolume
 
computeCriterion(Criterion) - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
computeDensity(ImageHandler, boolean) - Method in class mcib3d.image3d.processing.Density3D
 
computeDilate(ImageHandler, float, float, float) - Static method in class mcib3d.geom.interactions.Interactions
 
computeDistances(Point3D[]) - Method in class mcib3d.geom.Objects3DPopulation
 
computeEigen() - Method in class mcib3d.geom.Object3D
Constructor for the computeEigen object
computeFastRelationships() - Method in class mcib3d.geom.MereoAnalysis
 
computeHessianDerivative(int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
compute the hessian derivative (to validate)
computeInitialFeasibleSolution() - Method in class mcib3d.tracking_dev.HungarianAlgorithm
Compute an initial feasible solution by assigning zero labels to the workers and by assigning to each job a label equal to the minimum cost among its incident edges.
computeLines(ImageHandler) - Static method in class mcib3d.geom.interactions.Interactions
 
computeMassCenter(ImageHandler) - Method in class mcib3d.geom.Object3D
Compute the mass center of the object using signal from an image
computeMassCenter(ImageHandler, ImageHandler) - Method in class mcib3d.geom.Object3D
Compute the mass center of the object using signal from an image and within a mask
computeMassCenter(ImageHandler) - Method in class mcib3d.geom.Object3DFuzzy
 
computeMassCenter(ImageHandler) - Method in class mcib3d.geom.Object3DLabel
compute mass center with an image
computeMassCenter(ImageHandler, ImageHandler) - Method in class mcib3d.geom.Object3DLabel
 
computeMassCenter(ImageHandler) - Method in class mcib3d.geom.Object3DSurface
 
computeMassCenter(ImageHandler, ImageHandler) - Method in class mcib3d.geom.Object3DSurface
 
computeMassCenter(ImageHandler) - Method in class mcib3d.geom.Object3DVoxels
 
computeMassCenter(ImageHandler, ImageHandler) - Method in class mcib3d.geom.Object3DVoxels
 
computeMedian(List<Point3f>) - Method in class mcib3d.geom.deformation3d.Mesh
 
computeMeshSurface(boolean) - Method in class mcib3d.geom.Object3D
Deprecated.
use Object3D-IJUtils
computeMeshSurface(boolean) - Method in class mcib3d.geom.Object3DSurface
Deprecated.
computeMeshSurface(Object3D, boolean) - Static method in class mcib3d.geom.Viewer3D_Utils
 
computeMinMax() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
compute the min and max pixels
computeMoments2(boolean) - Method in class mcib3d.geom.Object3D
Compute the moments of the object (for ellipsoid orientation), order 2
computeMoments2(boolean) - Method in class mcib3d.geom.Object3DFuzzy
 
computeMoments2(boolean) - Method in class mcib3d.geom.Object3DLabel
Computation of the dispersion tensor with units value
computeMoments2(boolean) - Method in class mcib3d.geom.Object3DSurface
 
computeMoments2(boolean) - Method in class mcib3d.geom.Object3DVoxels
Computation of the dispersion tensor with units value
computeMoments3() - Method in class mcib3d.geom.Object3D
Compute the moments of the object, order 3
computeMoments3() - Method in class mcib3d.geom.Object3DLabel
 
computeMoments3() - Method in class mcib3d.geom.Object3DSurface
 
computeMoments3() - Method in class mcib3d.geom.Object3DVoxels
 
computeMoments4() - Method in class mcib3d.geom.Object3D
Compute the moments of the object, order 4
computeMoments4() - Method in class mcib3d.geom.Object3DLabel
 
computeMoments4() - Method in class mcib3d.geom.Object3DSurface
 
computeMoments4() - Method in class mcib3d.geom.Object3DVoxels
 
computeMomentsInertia() - Method in class mcib3d.geom.Object3DLabel
Computation of the inertia tensor with units value
computeMomentsInertia() - Method in class mcib3d.geom.Object3DVoxels
Computation of the inertia tensor with units value
computeRotation(double, double) - Method in class mcib3d.align.Align2D
compute the rotation for the images.
computeRotation(boolean, double, double) - Method in class mcib3d.align.Align2D
compute the rotation for the images.
computeRotation2Images(ImageProcessor, ImageProcessor, double, double) - Static method in class mcib3d.align.Align2D
compute the rotation between 2 images in space domain
the second image is rotated in the allowed range and the rotation obtaining the best correlation coefficient is returned
computeRotation2ImagesFHT(ImageProcessor, ImageProcessor, double, double) - Static method in class mcib3d.align.Align2D
compute the rotation between 2 images using the Fourier Transform.
use the power spectrum to be free of translation
then convert to polar coordinate to compute rotation with cross-correlation
computeRotationOld(double, double) - Method in class mcib3d.align.Align2D
Description of the Method
computeSlowRelationships() - Method in class mcib3d.geom.MereoAnalysis
 
computeTriangleList(ArrayList<Integer>) - Method in class mcib3d.geom.deformation3d.Mesh
 
computeUniqueVertices() - Method in class mcib3d.geom.deformation3d.Mesh
 
computeUpdatedLabels(boolean) - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
computeUpdatedLabels - Variable in class mcib3d.image3d.regionGrowing.Watershed3D_old
 
computeVertexList(ArrayList<Integer>) - Method in class mcib3d.geom.deformation3d.Mesh
 
computeVerticesNormals(List<Integer>) - Method in class mcib3d.geom.deformation3d.Mesh
 
computeVerticesNormals() - Method in class mcib3d.geom.Object3DSurface
 
computeVerticesNormalsWeighted() - Method in class mcib3d.geom.Object3DSurface
 
computeVolumes(boolean) - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
computeVolumes - Variable in class mcib3d.image3d.regionGrowing.Watershed3D_old
 
concat(ArrayUtil) - Method in class mcib3d.utils.ArrayUtil
concat an array to the end
cond() - Method in class mcib3d.Jama.Matrix
Matrix condition (2 norm)
cond() - Method in class mcib3d.Jama.SingularValueDecomposition
Two norm condition number
connect2DByteXY(ImageByte, int, IntCoord3D, byte, byte, byte) - Static method in class mcib3d.image3d.processing.Flood3D
Connect in 3D pixel with low values to pixel with high values Pixels with low values not connected to pixels with high values will remain with low values
connect3D(ImageInt, int, int) - Static method in class mcib3d.image3d.processing.Flood3D
 
connect3D(ImageHandler, int, int, boolean) - Static method in class mcib3d.image3d.processing.Flood3D
 
connect3DByteMultiZ(ImageByte, IntCoord3D, byte, byte, byte) - Static method in class mcib3d.image3d.processing.Flood3D
 
ConnectionThresholding_ - Class in mcib_plugins
Adjusts the lower and upper threshold levels of the active image.
ConnectionThresholding_() - Constructor for class mcib_plugins.ConnectionThresholding_
Constructor for the ThresholdAdjuster object
constructWithCopy(double[][]) - Static method in class mcib3d.Jama.Matrix
Construct a matrix from a copy of a 2-D array.
contains(String) - Method in class mcib3d.geom.interactions.InteractionsList
 
contains(int, int) - Method in class mcib3d.geom.interactions.InteractionsList
 
contains(int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
contains(double, double, double) - Method in class mcib3d.image3d.ImageHandler
 
contains(Voxel3D) - Method in class mcib3d.image3d.ImageHandler
 
contains(Point3DInt) - Method in class mcib3d.image3d.ImageHandler
 
contains(AssociationRegion) - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
contains(int) - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
contains(int) - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
containsOnly(ArrayList<Integer>) - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
contentAdded(Content) - Method in class mcib_plugins.tools.RoiManager3D_2
 
contentChanged(Content) - Method in class mcib_plugins.tools.RoiManager3D_2
 
contentRemoved(Content) - Method in class mcib_plugins.tools.RoiManager3D_2
 
contentSelected(Content) - Method in class mcib_plugins.tools.RoiManager3D_2
 
continueWatershed3D(int) - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
Compute the watershed image as next iteration from previous watershed , only for voxels with value > threshold
contours - Variable in class mcib3d.geom.Object3D
Contours pixels
convert(float[], boolean) - Static method in class mcib3d.image3d.ImageByte
 
convert(short[], boolean) - Static method in class mcib3d.image3d.ImageByte
 
convert(short[]) - Static method in class mcib3d.image3d.ImageFloat
 
convert(byte[]) - Static method in class mcib3d.image3d.ImageFloat
 
convert(float[], boolean) - Static method in class mcib3d.image3d.ImageShort
convert from float array to short array
convert(byte[]) - Static method in class mcib3d.image3d.ImageShort
convert from byte array to short array
convertToByte(boolean) - Method in class mcib3d.image3d.ImageFloat
 
convertToByte(ImageHandler[]) - Static method in class mcib3d.image3d.ImageHandler
 
convertToByte(ImageHandler) - Static method in class mcib3d.image3d.ImageHandler
 
convertToByte(boolean) - Method in class mcib3d.image3d.ImageShort
Convert to byte image
convertToByte(double) - Method in class mcib3d.image3d.ImageShort
Convert to byte image using saturation of the values
convertToFloat(boolean) - Method in class mcib3d.image3d.ImageByte
 
convertToFloat(boolean) - Method in class mcib3d.image3d.ImageShort
Convert to float 32 bit image
convertToShort(boolean) - Method in class mcib3d.image3d.ImageByte
 
convertToShort(boolean) - Method in class mcib3d.image3d.ImageFloat
 
Convex_Hull3D - Class in mcib_plugins
plugin to compute the 3D hull, based on quickHull
Convex_Hull3D() - Constructor for class mcib_plugins.Convex_Hull3D
 
convolve(double[], double) - Method in class mcib3d.utils.ArrayUtil
Convolution with a kernel
Coordinate3D - Class in mcib3d.image3d
 
Coordinate3D(int, int, int, int) - Constructor for class mcib3d.image3d.Coordinate3D
 
coords - Variable in class mcib3d.image3d.MaskIterator
Deprecated.
 
copy(ImageByte) - Method in class mcib3d.image3d.ImageByte
 
copy(ImageFloat) - Method in class mcib3d.image3d.ImageFloat
 
copy(ImageShort) - Method in class mcib3d.image3d.ImageShort
Copy the pixels values into the parameter image
copy() - Method in class mcib3d.Jama.Matrix
Make a deep copy of a matrix
copyObject(int) - Method in class mcib3d.geom.Object3DVoxels
 
copyParameters(DeformableMesh) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
CopyTomocoms() - Method in class mcib3d.ext.Imod
Description of the Method
correlation(ImageProcessor, ImageProcessor, double, double) - Static method in class mcib3d.align.Align2D
compute the correlation between 2 images
cost(Object3D, Object3D) - Method in interface mcib3d.tracking_dev.AssociationCost
 
cost(Object3D, Object3D) - Method in class mcib3d.tracking_dev.CostColoc2
 
cost(Object3D, Object3D) - Method in class mcib3d.tracking_dev.CostColocalisation
 
cost(Object3D, Object3D) - Method in class mcib3d.tracking_dev.CostPairMitosis
 
cost(Object3D, Object3D) - Method in class mcib3d.tracking_dev.CostTouching
 
CostColoc2 - Class in mcib3d.tracking_dev
 
CostColoc2() - Constructor for class mcib3d.tracking_dev.CostColoc2
 
CostColocalisation - Class in mcib3d.tracking_dev
 
CostColocalisation(Objects3DPopulation, Objects3DPopulation, double) - Constructor for class mcib3d.tracking_dev.CostColocalisation
 
CostesAutoThr() - Method in class mcib3d.image3d.processing.ImageColocalizer
 
CostesRand(int, int, int, double, int, boolean, boolean, boolean) - Method in class mcib3d.image3d.processing.ImageColocalizer
 
CostPairMitosis - Class in mcib3d.tracking_dev
 
CostPairMitosis() - Constructor for class mcib3d.tracking_dev.CostPairMitosis
 
CostPairMitosis(InteractionsList) - Constructor for class mcib3d.tracking_dev.CostPairMitosis
 
CostTouching - Class in mcib3d.tracking_dev
 
CostTouching(InteractionsList) - Constructor for class mcib3d.tracking_dev.CostTouching
 
couleur - Variable in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Description of the Field
countMaskVolume() - Method in class mcib3d.image3d.ImageByte
 
countMaskVolume() - Method in class mcib3d.image3d.ImageInt
 
countMaskVolume() - Method in class mcib3d.image3d.ImageShort
 
countValue(double) - Method in class mcib3d.utils.ArrayUtil
 
countValueAbove(double) - Method in class mcib3d.utils.ArrayUtil
 
createBrick(Vector3D, double, double, double, float) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createBrick(int, int, int, int, int, int, float) - Method in class mcib3d.geom.ObjectCreator3D
Create brick with bounding box coordinates, in Z direction
createBrick(int, int, int, double, double, double, float) - Method in class mcib3d.geom.ObjectCreator3D
Create a brick in Z direction with centre and radius
createBrickAxes(int, int, int, double, double, double, float, Matrix) - Method in class mcib3d.geom.ObjectCreator3D
Creation d'une ellipsoide
createBrickAxes(int, int, int, double, double, double, float, Vector3D) - Method in class mcib3d.geom.ObjectCreator3D
 
createBrickAxesUnit(double, double, double, double, double, double, float, Vector3D) - Method in class mcib3d.geom.ObjectCreator3D
 
createBrickUnit(Vector3D, double, double, double, float) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createBrickUnit(double, double, double, double, double, double, float) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createCone(int, int, int, double, double, double, double, double, float) - Method in class mcib3d.geom.ObjectCreator3D
 
createConeAxes(int, int, int, double, double, double, double, double, float, Matrix) - Method in class mcib3d.geom.ObjectCreator3D
 
createConeAxes(int, int, int, double, double, double, double, double, float, Vector3D, Vector3D) - Method in class mcib3d.geom.ObjectCreator3D
 
createConvexDaughters(Object3D, Object3D) - Static method in class mcib3d.tracking_dev.Mitosis
 
createCylinder(int, int, int, double, double, double, float) - Method in class mcib3d.geom.ObjectCreator3D
Creation d'un cylindre
createCylinderAxes(int, int, int, double, double, double, float, Matrix) - Method in class mcib3d.geom.ObjectCreator3D
Creation d'un cylindre
createCylinderAxes(int, int, int, double, double, double, float, Vector3D, Vector3D) - Method in class mcib3d.geom.ObjectCreator3D
 
createEllipsoid(Vector3D, double, double, double, float) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createEllipsoid(int, int, int, double, double, double, float, boolean) - Method in class mcib3d.geom.ObjectCreator3D
Creation d'une ellipsoide
createEllipsoidAxes(int, int, int, double, double, double, float, Matrix, boolean) - Method in class mcib3d.geom.ObjectCreator3D
Creation d'une ellipsoide (data in pix)
createEllipsoidAxesUnit(double, double, double, double, double, double, float, Vector3D, Vector3D, boolean) - Method in class mcib3d.geom.ObjectCreator3D
 
createEllipsoidPixel(int, int, int, float, float, float) - Method in class mcib3d.geom.Object3DVoxels
 
createEllipsoidUnit(double, double, double, double, double, double, float, boolean) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createEllipsoidUnit(Vector3D, double, double, double, float) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createGradientCube(Vector3D, double, double, double, Gradient) - Method in class mcib3d.geom.ObjectCreator3D
Création d'un dégradé
createGradientCube(int, int, int, double, double, double, Gradient) - Method in class mcib3d.geom.ObjectCreator3D
Création d'un dégradé sur cube
createGradientSphere(Point3D, double, Gradient) - Method in class mcib3d.geom.ObjectCreator3D
Création d'un gradient sur sphère
createGradientSphere(int, int, int, double, Gradient) - Method in class mcib3d.geom.ObjectCreator3D
Création d'un gradient sur ellipsoïde
createImageSameSize3D() - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
createIntersectionImage(Object3D, int, int, int) - Method in class mcib3d.geom.Object3D
Create an intersection image around two objects
createIntersectionImage(Object3D, int, int) - Method in class mcib3d.geom.Object3D
Create an intersection image around two objects (with no extra borders)
createKDTreeCenters() - Method in class mcib3d.geom.Objects3DPopulation
 
createKernelBrick(int, int, int) - Static method in class mcib3d.image3d.processing.FastFilters3D
Create a kernel neighorhood as an ellipsoid
createKernelEllipsoid(float, float, float) - Static method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Create a kernel neighorhood as an ellipsoid
createKernelEllipsoid(float, float, float) - Static method in class mcib3d.image3d.processing.FastFilters3D
Create a kernel neighorhood as an ellipsoid
createKernelFromObject(Object3D) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
createKernelLoG_Base(double) - Method in class mcib_plugins.processing.LoG3D
 
createKernelLoG_Fact(double, double) - Method in class mcib_plugins.processing.LoG3D
 
createLine(int, int, int, int, int, int, float, int) - Method in class mcib3d.geom.ObjectCreator3D
Create a 3D line
createLine(Vector3D, Vector3D, float, int) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createLine(Point3D, Point3D, float, int) - Method in class mcib3d.geom.ObjectCreator3D
 
createLineUnit(Vector3D, Vector3D, float, int) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createListVoxels(int) - Method in class mcib3d.image3d.ImageHandler
 
createLocalMaximaImage(float, float, float, boolean) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Create a image with local maxima
createLocalMaximaImage(float, float, float, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Création d'une image des maxima locaux dans un voisinage donne
createLocalMaximaImage(float, float, float, int, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Création d'une image des maxima locaux dans un voisiange donne
createLocalMaximaImage(float, float, float, boolean) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Création d'une image des maxima locaux dans un voisiange donne
createMask(ImagePlus) - Static method in class mcib_plugins.analysis.spatialAnalysis
 
createObject3DLabel(ImagePlus, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
createObject3DLabel(ImageStack, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
createObject3DVoxels(ImagePlus, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
createObject3DVoxels(ImageStack, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
createOFF(List<Integer>) - Method in class mcib3d.geom.deformation3d.Mesh
 
createPixel(int, int, int, int) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createRandomPopulation(int, double) - Method in class mcib3d.geom.Objects3DPopulation
 
createRandomPopulationDistAbsMb(int, double, double) - Method in class mcib3d.geom.Objects3DPopulation
 
createRoi(int) - Method in class mcib3d.geom.Object3D
Deprecated.
use Object3D-IJUtils create a roi for a slice
createRoi(Object3D, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
createRoi(int) - Method in class mcib3d.geom.Object3DFuzzy
 
createRoi(int) - Method in class mcib3d.geom.Object3DLabel
Deprecated.
createRoi(int) - Method in class mcib3d.geom.Object3DSurface
Deprecated.
createRoi(int) - Method in class mcib3d.geom.Object3DVoxels
Deprecated.
use Object3D-IJUtils Constructor for the createRoi object
createSameDimensions() - Method in class mcib3d.image3d.ImageHandler
 
createSameType(int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
createSegImage(int, int, int, int, int, int, int) - Method in class mcib3d.geom.Object3D
 
createSegImage(int, int, int) - Method in class mcib3d.geom.Object3D
 
createSegImageMini2D(int, int) - Method in class mcib3d.geom.Object3D
 
createSphere(GeomTransform3D, int, int) - Static method in class mcib3d.geom.Object3DSurface
 
createSphere(double, double, double, double, float, boolean) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createSphereUnit(float, float, float, float) - Method in class mcib3d.geom.Object3DVoxels
 
createSphereUnit(double, double, double, double, float, boolean) - Method in class mcib3d.geom.ObjectCreator3D
Description of the Method
createThreadArray(int) - Static method in class mcib3d.utils.ThreadUtil
 
createThreadArray() - Static method in class mcib3d.utils.ThreadUtil
 
CreateXf(double[], double[], double[], String) - Method in class mcib3d.ext.Imod
Constructor for the CreateXf object
CreateXf(double, double[][], int, String) - Method in class mcib3d.ext.Imod
Create a Xf file for a given angle of rotation and shifts
CreateXf(double, int, String) - Method in class mcib3d.ext.Imod
Description of the Method
CRITERIA_METHOD_MAX_CLASSIFICATION - Static variable in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
CRITERIA_METHOD_MAX_COMPACTNESS - Static variable in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
CRITERIA_METHOD_MAX_EDGES - Static variable in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
CRITERIA_METHOD_MAX_VOLUME - Static variable in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
CRITERIA_METHOD_MIN_ELONGATION - Static variable in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
CRITERIA_METHOD_MSER - Static variable in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
Criterion - Interface in mcib3d.image3d.IterativeThresholding
Created by thomasb on 20/4/16.
CriterionClassification - Class in mcib3d.image3d.IterativeThresholding
 
CriterionClassification(String) - Constructor for class mcib3d.image3d.IterativeThresholding.CriterionClassification
 
CriterionCompactness - Class in mcib3d.image3d.IterativeThresholding
Created by thomasb on 20/4/16.
CriterionCompactness() - Constructor for class mcib3d.image3d.IterativeThresholding.CriterionCompactness
 
CriterionEdge - Class in mcib3d.image3d.IterativeThresholding
Created by thomasb on 20/4/16.
CriterionEdge(ImageHandler, double) - Constructor for class mcib3d.image3d.IterativeThresholding.CriterionEdge
 
CriterionElongation - Class in mcib3d.image3d.IterativeThresholding
Created by thomasb on 20/4/16.
CriterionElongation() - Constructor for class mcib3d.image3d.IterativeThresholding.CriterionElongation
 
CriterionVolume - Class in mcib3d.image3d.IterativeThresholding
Created by thomasb on 20/4/16.
CriterionVolume() - Constructor for class mcib3d.image3d.IterativeThresholding.CriterionVolume
 
crop(int, int, int, int, int, int) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Cropping of the image
crop(int, int, int, int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
crop3D(String, int, int, int, int, int, int) - Method in class mcib3d.image3d.BlankMask
 
crop3D(TreeMap<Float, int[]>) - Method in class mcib3d.image3d.BlankMask
 
crop3D(String, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageByte
 
crop3D(TreeMap<Float, int[]>) - Method in class mcib3d.image3d.ImageByte
 
crop3D(String, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageFloat
 
crop3D(TreeMap<Float, int[]>) - Method in class mcib3d.image3d.ImageFloat
 
crop3D(String, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
crop3D(TreeMap<Float, int[]>) - Method in class mcib3d.image3d.ImageHandler
 
crop3D(String, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageInt
 
crop3D(TreeMap<Float, int[]>) - Method in class mcib3d.image3d.ImageInt
 
crop3D(String, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageShort
 
crop3D(TreeMap<Float, int[]>) - Method in class mcib3d.image3d.ImageShort
 
Crop3D_ - Class in mcib_plugins
plugin de crop 3D
Crop3D_() - Constructor for class mcib_plugins.Crop3D_
 
Crop3D_All - Class in mcib_plugins
plugin de crop 3D
Crop3D_All() - Constructor for class mcib_plugins.Crop3D_All
 
crop3DBinary(String, float, int, int, int, int, int, int) - Method in class mcib3d.image3d.BlankMask
 
crop3DBinary(String, float, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageByte
 
crop3DBinary(String, float, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageInt
 
crop3DBinary(TreeMap<Float, int[]>) - Method in class mcib3d.image3d.ImageInt
 
crop3DBinary() - Method in class mcib3d.image3d.ImageInt
 
crop3DBinary(String, float, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageShort
 
crop3DMask(String, ImageInt, float, int, int, int, int, int, int) - Method in class mcib3d.image3d.BlankMask
 
crop3DMask(String, ImageInt, float, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageByte
 
crop3DMask(String, ImageInt, float, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageFloat
 
crop3DMask(String, ImageInt, float, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
crop3DMask(String, ImageInt, float, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageInt
 
crop3DMask(String, ImageInt, float, int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageShort
 
cropRadius(int, int, int, int, int, int, boolean, boolean) - Method in class mcib3d.image3d.ImageFloat
 
cropRadius(int, int, int, int, int, int, boolean, boolean) - Method in class mcib3d.image3d.ImageHandler
Extract a 3D image from a specified location as the center of crop
cropRadius(int, int, int, int, int, int, boolean, boolean) - Method in class mcib3d.image3d.ImageInt
 
crossCorrelation(ImageProcessor, ImageProcessor) - Static method in class mcib3d.align.Align2D
computes the crosscorrelation between 2 images using FFT
crossCorrelation(ImageProcessor, ImageProcessor, int, int) - Static method in class mcib3d.align.Align2D
compute the crosscorrelation between 2 images with a maximum translation of (maxX,maxY)
crossCorrelation(ImageStack, ImageStack) - Static method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Cross Correlation 3D on ImageStack
crossCorrelation(Image3D, Image3D) - Static method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Cross Correlation 3D on Image3D
crossCorrelationNormalized(Image3D, int, int, int, int, int, int, int, int, int) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Cross correlation between this image and another one at a specified location .
crossProduct(Point3f, Point3f) - Method in class mcib3d.geom.deformation3d.Mesh
 
crossProduct(Vector3D) - Method in class mcib3d.geom.Vector3D
the cross product between two vectors
currentMask - Variable in class mcib3d.image3d.ImageLabeller
 
currentMask - Variable in class mcib3d.image3d.ImageLabeller2D
 
currentQuantifImage - Variable in class mcib3d.geom.Object3D
current image used for quantification (to compute results once)
cx - Variable in class mcib3d.geom.Object3D
Center of mass x
cy - Variable in class mcib3d.geom.Object3D
Center of mass y
CytoFluo() - Method in class mcib3d.image3d.processing.ImageColocalizer
 
cz - Variable in class mcib3d.geom.Object3D
Center of mass z

D

d - Variable in class mcib3d.image3d.distanceMap3d.CleanUpLocalThickness
Deprecated.
 
d - Variable in class mcib3d.image3d.distanceMap3d.DistanceRidge
Deprecated.
 
d - Variable in class mcib3d.image3d.distanceMap3d.LocalThickness
Deprecated.
 
Data - Class in mcib3d.Classification
 
Data(DataSet) - Constructor for class mcib3d.Classification.Data
 
data - Variable in class mcib3d.image3d.distanceMap3d.DistanceRidge
Deprecated.
 
data - Variable in class mcib3d.image3d.distanceMap3d.LocalThickness
Deprecated.
 
DataSet - Class in mcib3d.Classification
 
DataSet(String, Attributes) - Constructor for class mcib3d.Classification.DataSet
 
DC - Static variable in class mcib3d.geom.MereoObject3D
 
debug_show_filter_mask_array() - Method in class mcib_plugins.Filter3D.Kernel3D
 
debug_show_kernel(int) - Method in class mcib_plugins.Filter3D.Kernel3D
 
debug_show_offset_matrix() - Method in class mcib_plugins.Filter3D.Kernel3D
 
deCalibrateObject() - Method in class mcib3d.geom.Object3DSurface
 
decenter() - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Description of the Method
DeformableMesh - Class in mcib3d.geom.deformation3d
/** Copyright (C) 2008- 2012 Thomas Boudier and others This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
DeformableMesh(List<Point3f>, int) - Constructor for class mcib3d.geom.deformation3d.DeformableMesh
 
DeformableMesh(List<Point3f>) - Constructor for class mcib3d.geom.deformation3d.DeformableMesh
 
defZoomFactor - Static variable in class mcib3d.image3d.ImageHandler
 
delay() - Method in class mcib3d.utils.Chrono
Description of the Method
delayString() - Method in class mcib3d.utils.Chrono
Description of the Method
deleteImage(int) - Method in class mcib3d.align.Align2D
Description of the Method
deleteSlices(int, int) - Method in class mcib3d.image3d.ImageByte
 
deleteSlices(int, int) - Method in class mcib3d.image3d.ImageFloat
 
deleteSlices(int, int) - Method in class mcib3d.image3d.ImageHandler
 
deleteSlices(int, int) - Method in class mcib3d.image3d.ImageShort
 
Density3D - Class in mcib3d.image3d.processing
 
Density3D(int, double) - Constructor for class mcib3d.image3d.processing.Density3D
 
Density3D_ - Class in mcib_plugins
 
Density3D_() - Constructor for class mcib_plugins.Density3D_
 
Deriche - Class in mcib3d.geom.deformation3d
 
Deriche(ImageStack) - Constructor for class mcib3d.geom.deformation3d.Deriche
 
Deriche(ImageStack, double[]) - Constructor for class mcib3d.geom.deformation3d.Deriche
 
desactivateAverage(int) - Method in class mcib3d.align.Align3D
Description of the Method
desactivateAverageAll() - Method in class mcib3d.align.Align3D
Description of the Method
det() - Method in class mcib3d.Jama.LUDecomposition
Determinant
det() - Method in class mcib3d.Jama.Matrix
Matrix determinant
detectAndMergeSplit() - Method in class mcib3d.tracking_dev.MitosisDetector
 
detectMitosis() - Method in class mcib3d.tracking_dev.MitosisDetector
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class mcib_plugins.Fast_filters3D
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class mcib_plugins.Filters3d_jni
 
DIFF - Static variable in class mcib3d.image3d.processing.FastArithmetic3D
 
diffAbsImage(ImageHandler) - Method in class mcib3d.image3d.ImageInt
 
difference_kernel_offset_matrix - Variable in class mcib_plugins.Filter3D.Kernel3D
 
dilatation3D(float, float, float, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
3D dilatation
dilatation3D(Image3D, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
3D dilatation with kernel
dilatation3D(int, int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
base pour la morphologie mathématique binaire (dilatation)
Les objets sont segmentes et ont donc une couleur différente du fond
dilatationConditionGris(IntImage3D, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Dilatation par rapport a une image de base
dilate(float, ImageInt, int) - Method in class mcib3d.geom.Object3DVoxels
 
Disconnection() - Method in class mcib3d.geom.MereoObject3D
 
Discrete() - Method in class mcib3d.geom.MereoObject3D
 
disjointBox(Object3D) - Method in class mcib3d.geom.Object3D
 
distance(Point3f, Point3f) - Method in class mcib3d.geom.deformation3d.Mesh
 
distance(Point3D) - Method in class mcib3d.geom.Point3D
Description of the Method
distance(Point3D, double, double) - Method in class mcib3d.geom.Point3D
Description of the Method
distance(Vector3D) - Method in class mcib3d.geom.Vector3D
Distance between two vectors
distance(double[], double[]) - Method in class mcib3d.utils.KDTreeC
Compares arrays of double and returns the euclidean distance between them.
DistanceRidge - Class in mcib3d.image3d.distanceMap3d
Deprecated.
DistanceRidge() - Constructor for class mcib3d.image3d.distanceMap3d.DistanceRidge
Deprecated.
 
Distances_ - Class in mcib_plugins
 
Distances_() - Constructor for class mcib_plugins.Distances_
 
distancesAllBorder() - Method in class mcib3d.geom.Objects3DPopulation
 
distancesAllCenter() - Method in class mcib3d.geom.Objects3DPopulation
 
distancesAllClosestBorder() - Method in class mcib3d.geom.Objects3DPopulation
 
distancesAllClosestCenter() - Method in class mcib3d.geom.Objects3DPopulation
 
distancesAllPairsBorder(Objects3DPopulation) - Method in class mcib3d.geom.Objects3DPopulation
All distances 2x2 from center to center
distancesAllPairsBorder() - Method in class mcib3d.geom.Objects3DPopulation
All distances 2x2 from border to border
distancesAllPairsCenter() - Method in class mcib3d.geom.Objects3DPopulation
All distances 2x2 from center to center
distancesAllPairsCenter(Objects3DPopulation) - Method in class mcib3d.geom.Objects3DPopulation
All distances 2x2 from center to center
distanceSq(double[], double[]) - Method in class mcib3d.utils.KDTreeC
Compares arrays of double and returns the squared euclidean distance between them.
distanceSq - Variable in class mcib3d.utils.KDTreeC.Item
 
distanceSquare(Point3D) - Method in class mcib3d.geom.Point3D
Description of the Method
distanceSquare(Point3D, double, double) - Method in class mcib3d.geom.Point3D
Description of the Method
distanceSquare(Vector3D) - Method in class mcib3d.geom.Vector3D
Description of the Method
distBB - Variable in class mcib3d.geom.MereoObject3D
 
distBlock(Point3D) - Method in class mcib3d.geom.Point3D
 
distBorderPixel(Object3D) - Method in class mcib3d.geom.Object3D
the minimum distance between two objets (in real distance) computed on the contours pixels
distBorderUnit(Object3D) - Method in class mcib3d.geom.Object3D
the minimum distance between two objets (in real distance) computed on the contours pixels
distBorderUnit(Point3D, Object3D, Point3D, boolean) - Method in class mcib3d.geom.Object3D
The border to border distance along a direction (EXPERIMENTAL)
distCenter2DUnit(Object3D) - Method in class mcib3d.geom.Object3D
2D distance from center to center (in real distance)
distCenterBorderUnit(Object3D) - Method in class mcib3d.geom.Object3D
Distance center of this object to the border of the other
distCenterPixel(Object3D) - Method in class mcib3d.geom.Object3D
distance from center to center (in pixel)
distCenterUnit(Object3D) - Method in class mcib3d.geom.Object3D
distance from center to center (in real distance)
distHausdorffUnit(Object3D) - Method in class mcib3d.geom.Object3D
 
distinctValues() - Method in class mcib3d.utils.ArrayUtil
Array with only distinct values (sorted)
distPixelBorder(Point3D) - Method in class mcib3d.geom.Object3D
 
distPixelBorderUnit(double, double, double) - Method in class mcib3d.geom.Object3D
Distance from a point to the border of the object
distPixelBorderUnit(double, double, double, Vector3D) - Method in class mcib3d.geom.Object3D
Distance from a point along a direction to the border of the object
distPixelCenter(double, double, double) - Method in class mcib3d.geom.Object3D
The distance between center and a point with coordinates
distPixelCenter(Point3D) - Method in class mcib3d.geom.Object3D
The distance between center and a Point3D
divideAll(double) - Method in class mcib3d.utils.ArrayUtil
 
divideBy(float) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
divides all pixels by a value
divideByValue(float) - Method in class mcib3d.image3d.ImageHandler
 
divideImage(ImageHandler, float) - Method in class mcib3d.image3d.ImageHandler
Compute the operation this/(other*coeff);
doForwardTransform() - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Description of the Method
doHyst(ImagePlus, double, double, int, int) - Method in class mcib_plugins.ConnectionThresholding_
Hysteresis thresholding for stack or image
doInverseTransform() - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Description of the Method
doLoG(ImageWare, double, double) - Method in class mcib_plugins.processing.LoG3D
 
doLoG(ImageWare, double, double, double) - Method in class mcib_plugins.processing.LoG3D
 
doLoG_Separable(ImageWare, double, double) - Method in class mcib_plugins.processing.LoG3D
 
doLoG_Separable(ImageWare, double, double, double) - Method in class mcib_plugins.processing.LoG3D
 
doRFA(double, double) - Method in class mcib3d.align.Align2D
align all images using RFA procedure (Penczek 1992)
dotProduct(Point3f, Point3f) - Method in class mcib3d.geom.deformation3d.Mesh
 
dotProduct(Vector3D) - Method in class mcib3d.geom.Vector3D
scalar product between two vectors
dotProduct(Vector3D, double, double) - Method in class mcib3d.geom.Vector3D
Compute the scalar product, using calibration
doTrin(ImagePlus, double, double, int, int) - Method in class mcib_plugins.ConnectionThresholding_
Multi thresholding for stack or image
dragEnter(DropTargetDragEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
dragExit(DropTargetEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
dragOver(DropTargetDragEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
draw(ObjectCreator3D, int) - Method in class mcib3d.geom.Object3D
drawing inside an objectCreator
draw(ByteProcessor, int, int) - Method in class mcib3d.geom.Object3D
Deprecated.
use Object3D-IJUtils drawing inside a 2D byteprocessor
draw(ImageStack, int) - Method in class mcib3d.geom.Object3D
Deprecated.
use Object3D-IJUtils drawing inside an imagestack
draw(ImageHandler, float) - Method in class mcib3d.geom.Object3D
drawing inside an ImageHandler
draw(ImageHandler, int, int, int, int) - Method in class mcib3d.geom.Object3D
 
draw(ImageHandler) - Method in class mcib3d.geom.Object3D
Drawing inside an image, with default value = object value
draw(ImageStack, int, int, int) - Method in class mcib3d.geom.Object3D
Deprecated.
use Object3D-IJUtils drawing inside an imagestack, in rgb color
draw(Object3D, ByteProcessor, int, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
draw(Object3D, ImageStack, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
draw(Object3D, ImageStack, int, int, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
draw(ImageStack, int) - Method in class mcib3d.geom.Object3DFuzzy
 
draw(ImageStack, int, int, int) - Method in class mcib3d.geom.Object3DFuzzy
 
draw(ByteProcessor, int, int) - Method in class mcib3d.geom.Object3DFuzzy
 
draw(ObjectCreator3D, int) - Method in class mcib3d.geom.Object3DLabel
Draw the pixel inside a creator
draw(ByteProcessor, int, int) - Method in class mcib3d.geom.Object3DLabel
Deprecated.
draw(ImageHandler, int) - Method in class mcib3d.geom.Object3DLabel
 
draw(ImageHandler, float) - Method in class mcib3d.geom.Object3DLabel
 
draw(ImageStack, int, int, int) - Method in class mcib3d.geom.Object3DLabel
Deprecated.
draw(ImageStack, int) - Method in class mcib3d.geom.Object3DLabel
Deprecated.
draw(ImageHandler, int, int, int, int) - Method in class mcib3d.geom.Object3DLabel
 
draw(ObjectCreator3D, int) - Method in class mcib3d.geom.Object3DSurface
 
draw(ByteProcessor, int, int) - Method in class mcib3d.geom.Object3DSurface
Deprecated.
draw(ImageStack, int) - Method in class mcib3d.geom.Object3DSurface
Deprecated.
draw(ImageHandler, float) - Method in class mcib3d.geom.Object3DSurface
 
draw(ImageHandler, int, int, int, int) - Method in class mcib3d.geom.Object3DSurface
 
draw(ImageStack, int, int, int) - Method in class mcib3d.geom.Object3DSurface
Deprecated.
draw(ObjectCreator3D, int) - Method in class mcib3d.geom.Object3DVoxels
Draw the pixel inside a creator
draw(ByteProcessor, int, int) - Method in class mcib3d.geom.Object3DVoxels
Deprecated.
use Object3D-IJUtils Draw inside a particular Z
draw(ImageStack, int) - Method in class mcib3d.geom.Object3DVoxels
Deprecated.
use Object3D-IJUtils
draw(ImageStack, int, int, int) - Method in class mcib3d.geom.Object3DVoxels
Deprecated.
use Object3D-IJUtils
draw(ImageHandler, float) - Method in class mcib3d.geom.Object3DVoxels
 
draw(ImageHandler, int, int, int, int) - Method in class mcib3d.geom.Object3DVoxels
 
draw(ImageStack, int) - Method in class mcib3d.geom.Objects3DPopulation
 
draw(ImageStack) - Method in class mcib3d.geom.Objects3DPopulation
 
draw(Object3D, int) - Method in class mcib3d.image3d.BlankMask
 
draw(Object3D, float) - Method in class mcib3d.image3d.ImageByte
 
draw(Object3D, int) - Method in class mcib3d.image3d.ImageByte
 
draw(Object3D, float) - Method in class mcib3d.image3d.ImageFloat
 
draw(Object3D, float) - Method in class mcib3d.image3d.ImageHandler
 
draw(Object3D, int) - Method in class mcib3d.image3d.ImageInt
 
draw(Object3D, float) - Method in class mcib3d.image3d.ImageShort
 
draw(Object3D, int) - Method in class mcib3d.image3d.ImageShort
 
Draw_RoiSlices - Class in mcib_plugins.tools
* /** Copyright (C) 2008- 2012 Thomas Boudier and others
Draw_RoiSlices() - Constructor for class mcib_plugins.tools.Draw_RoiSlices
 
drawAbout() - Method in class mcib3d.utils.AboutMCIB
draw the window
drawAssociation(ImageHandler) - Method in class mcib3d.tracking_dev.Association
Deprecated.
drawAssociationPath(ImageHandler, ImageHandler, ImageHandler) - Method in class mcib3d.tracking_dev.Association
Deprecated.
drawAt(ImageHandler, int, Point3D) - Method in class mcib3d.geom.Object3D
 
drawBar(int) - Method in class mcib3d.utils.ArrayUtil
drawing of the array as an image
drawContent(Image3DUniverse, Color3f, String) - Method in class mcib3d.geom.Object3DSurface
 
drawContours(ObjectCreator3D, int) - Method in class mcib3d.geom.Object3DFuzzy
 
drawContours(ObjectCreator3D, int) - Method in class mcib3d.geom.Object3DVoxels
 
drawContoursXY(ObjectCreator3D, int, int) - Method in class mcib3d.geom.Object3DVoxels
 
drawCurvature(ImageFloat, double[]) - Method in class mcib3d.geom.Object3DSurface
 
drawFacesCurvature(Image3DUniverse, double[], String, boolean) - Method in class mcib3d.geom.Object3DSurface
 
drawFacesVertex(int, Image3DUniverse, Color3f, String, boolean) - Method in class mcib3d.geom.Object3DSurface
 
drawGradient(Image3D) - Method in class mcib3d.geom.GradientPoint
 
drawIntersection(ImageStack, Object3DLabel, int, int, int) - Method in class mcib3d.geom.Object3DLabel
Deprecated.
drawIntersection(ImageStack, Object3DLabel, int) - Method in class mcib3d.geom.Object3DLabel
Deprecated.
drawIntersectionLabel(Object3DLabel, Object3DLabel, ImageStack, int, int, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
drawIntersectionLabel(Object3DLabel, Object3DLabel, ImageStack, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
drawLabel(Object3D, ImageStack, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
drawLabel(Object3D, ImageStack, int, int, int, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
drawLine(int, int, int, int, int, int, double) - Method in class mcib3d.geom.deformation3d.Deriche
 
drawLine(Point3f, Point3f, double) - Method in class mcib3d.geom.deformation3d.Deriche
 
drawLink(ImageHandler, Object3D, int) - Method in class mcib3d.geom.Object3D
Drawing links between two objects
drawMesh(ObjectCreator3D, int) - Method in class mcib3d.geom.Object3DSurface
 
drawNeighbors(int, Image3DUniverse, Color3f, String, boolean) - Method in class mcib3d.geom.Object3DSurface
 
drawNormal(int, double, Image3DUniverse, Color3f, String, boolean) - Method in class mcib3d.geom.Object3DSurface
 
drawObject(Object3D) - Method in class mcib3d.geom.ObjectCreator3D
 
drawOrphan1(ImageHandler) - Method in class mcib3d.tracking_dev.Association
Deprecated.
drawOrphan2(ImageHandler) - Method in class mcib3d.tracking_dev.Association
Deprecated.
drawPopulation() - Method in class mcib3d.geom.Objects3DPopulation
 
drawPopulation(int, int, int) - Method in class mcib3d.geom.Objects3DPopulation
 
drawRandomColors(Objects3DPopulation, int, int, int) - Static method in class mcib3d.geom.Object3D_IJUtils
 
drawVoxels(ArrayList<Voxel3D>) - Method in class mcib3d.geom.ObjectCreator3D
 
drop(DropTargetDropEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
dropActionChanged(DropTargetDragEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
duplicate() - Method in class mcib3d.image3d.ImageByte
 
duplicate() - Method in class mcib3d.image3d.ImageFloat
 
duplicate() - Method in class mcib3d.image3d.ImageHandler
 
duplicate() - Method in class mcib3d.image3d.ImageInt
 
duplicate() - Method in class mcib3d.image3d.ImageShort
 
duplicate() - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Description of the Method

E

EC - Static variable in class mcib3d.geom.MereoObject3D
 
EcritFichierAngles(int) - Method in class mcib3d.ext.Imod
Description of the Method
EcritFichierAngles(int, String) - Method in class mcib3d.ext.Imod
Création du fichier d'angles
EcritFichierParams(String) - Method in class mcib3d.ext.Imod
Création du fichier de param�res pour copytomocoms
EcritFichierParams() - Method in class mcib3d.ext.Imod
Description of the Method
EcritFichierXTilt(int, double, String) - Method in class mcib3d.ext.Imod
Création du fichier d'angles
EcritInfoTomo(String) - Method in class mcib3d.ext.Xmipp
Constructor for the EcritInfoTomo object
EcritScriptAlign(String, String) - Method in class mcib3d.ext.Xmipp
Description of the Method
EcritScriptReconstruction(String, String, String) - Method in class mcib3d.ext.Xmipp
Description of the Method
edgeContact(Object3D, int) - Method in class mcib3d.geom.Object3D
 
edgeImage(ImageHandler, boolean, boolean) - Method in class mcib3d.geom.Object3D
 
EDT - Class in mcib3d.image3d.distanceMap3d
 
EDT() - Constructor for class mcib3d.image3d.distanceMap3d.EDT
 
EDT_1D - Class in mcib3d.image3d.distanceMap3d
 
EDT_1D(ImageHandler) - Constructor for class mcib3d.image3d.distanceMap3d.EDT_1D
 
EDT_3D - Class in mcib_plugins
Euclidean Distance Map and Eroded Volume Fraction (originally written by Jean Ollion for TANGO)
EDT_3D() - Constructor for class mcib_plugins.EDT_3D
 
EdtByte - Class in mcib3d.image3d.distanceMap3d
 
EdtByte() - Constructor for class mcib3d.image3d.distanceMap3d.EdtByte
 
EdtByteInv - Class in mcib3d.image3d.distanceMap3d
 
EdtByteInv() - Constructor for class mcib3d.image3d.distanceMap3d.EdtByteInv
 
EdtFloat - Class in mcib3d.image3d.distanceMap3d
 
EdtFloat() - Constructor for class mcib3d.image3d.distanceMap3d.EdtFloat
 
EdtFloatInv - Class in mcib3d.image3d.distanceMap3d
 
EdtFloatInv() - Constructor for class mcib3d.image3d.distanceMap3d.EdtFloatInv
 
EdtShort - Class in mcib3d.image3d.distanceMap3d
 
EdtShort() - Constructor for class mcib3d.image3d.distanceMap3d.EdtShort
 
EdtShortInv - Class in mcib3d.image3d.distanceMap3d
 
EdtShortInv() - Constructor for class mcib3d.image3d.distanceMap3d.EdtShortInv
 
EdtShortLabel - Class in mcib3d.image3d.distanceMap3d
 
EdtShortLabel() - Constructor for class mcib3d.image3d.distanceMap3d.EdtShortLabel
 
eig() - Method in class mcib3d.Jama.Matrix
Eigenvalue Decomposition
eigen - Variable in class mcib3d.geom.Object3D
Matrix of decomposition
EigenvalueDecomposition - Class in mcib3d.Jama
Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(Matrix) - Constructor for class mcib3d.Jama.EigenvalueDecomposition
Check for symmetry, then construct the eigenvalue decomposition
Ellipsoids_3D - Class in mcib_plugins
plugin to fit an 3D ellipsoid to a shape
Ellipsoids_3D() - Constructor for class mcib_plugins.Ellipsoids_3D
 
EMPTY - Static variable in class mcib3d.geom.MereoObject3D
 
end - Variable in class mcib3d.utils.ThreadRunner
Start all given threads and wait on each of them until all are done.
enlarge(int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
EQ - Static variable in class mcib3d.geom.MereoObject3D
 
Equality() - Method in class mcib3d.geom.MereoObject3D
 
equals(Object) - Method in class mcib3d.geom.Point3D
 
equals(Object) - Method in class mcib3d.geom.Voxel3D
 
equals(Object) - Method in class mcib3d.image3d.BlankMask
 
equals(Object) - Method in class mcib3d.image3d.ImageLabeller.Vox3D
 
equals(Object) - Method in class mcib3d.image3d.ImageLabeller2D.Vox2D
 
equals(AssociationRegion) - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
erase() - Method in class mcib3d.image3d.BlankMask
 
erase() - Method in class mcib3d.image3d.ImageByte
 
erase() - Method in class mcib3d.image3d.ImageFloat
 
erase() - Method in class mcib3d.image3d.ImageHandler
 
erase() - Method in class mcib3d.image3d.ImageShort
 
Eraser2() - Method in class mcib3d.ext.Imod
Description of the Method
erode(float, int) - Method in class mcib3d.image3d.ImageInt
 
erosion3D(float, float, float, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Erosion binaire 3D, normalement les objets sont noir sur fond blanc
erosion3D(Image3D, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Erosion binaire 3D avec kernel, normalement les objets sont noir sur fond blanc
erosion3D(int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Erosion binaire 3D, normalement les objets sont noir sur fond blanc
erosion3D(Image3D) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Erosion binaire 3D avec kernel, normalement les objets sont noir sur fond blanc
erosion3D(int, int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
error() - Method in class mcib3d.Classification.Classifier
 
evaluate(double) - Method in class mcib3d.geom.Gradient
Corrige la valeur du pourcentage en fonction de la loi à suivre
EVF_Radial - Class in mcib_plugins
 
EVF_Radial() - Constructor for class mcib_plugins.EVF_Radial
 
exceptionPrinter - Class in mcib3d.utils
 
exceptionPrinter() - Constructor for class mcib3d.utils.exceptionPrinter
 
execute() - Method in class mcib3d.tracking_dev.HungarianAlgorithm
Execute the algorithm.
executePhase() - Method in class mcib3d.tracking_dev.HungarianAlgorithm
Execute a single phase of the algorithm.
extendHisto() - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
extension de l'histogramme sur chaque couleur
extendHisto() - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
extension de l'histogramme de l'image 8 bits
ExternalConnection() - Method in class mcib3d.geom.MereoObject3D
 
extract(int, int, int, int, int, int, boolean) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Extract a 3D image from a specified location as the center of crop
extractCurrentStack(ImagePlus) - Static method in class mcib3d.image3d.ImagePlus_Utils
 
extractLine(int, int, int, int, int, int) - Method in class mcib3d.geom.deformation3d.Deriche
 
extractLine(int, int, int, int, int, int, boolean) - Method in class mcib3d.image3d.ImageHandler
 
ExtractShiftsFromXG(String, String, int) - Method in class mcib3d.ext.Imod
Description of the Method

F

F_Function - Class in mcib3d.spatial.descriptors
 
F_Function(int, Object3D) - Constructor for class mcib3d.spatial.descriptors.F_Function
 
faces - Variable in class mcib3d.geom.Object3DSurface
 
faces_vertices_index - Variable in class mcib3d.geom.Object3DSurface
 
facesNormals - Variable in class mcib3d.geom.deformation3d.Mesh
 
Fast_filters3D - Class in mcib_plugins
3D filtering
Fast_filters3D() - Constructor for class mcib_plugins.Fast_filters3D
 
FastArithmetic3D - Class in mcib3d.image3d.processing
* /** Copyright (C) 2008- 2012 Thomas Boudier and others
FastArithmetic3D() - Constructor for class mcib3d.image3d.processing.FastArithmetic3D
 
FastFilters3D - Class in mcib3d.image3d.processing
* /** Copyright (C) 2008- 2012 Thomas Boudier and others
FastFilters3D() - Constructor for class mcib3d.image3d.processing.FastFilters3D
 
FastOperation3D - Class in mcib3d.image3d.processing
* /** Copyright (C) 2008- 2012 Thomas Boudier and others
FastOperation3D() - Constructor for class mcib3d.image3d.processing.FastOperation3D
 
feret - Variable in class mcib3d.geom.Object3D
feret diameter
feret1 - Variable in class mcib3d.geom.Object3D
Pixel 1 for feret diameter
feret2 - Variable in class mcib3d.geom.Object3D
Pixel 2 for feret diameter
fermeture3D(int, int, int, int, boolean) - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Fermeture binaire 3D, normalement les objets sont noir sur fond blanc
fermeture3D(int, int, int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
fetchUnmatchedWorker() - Method in class mcib3d.tracking_dev.HungarianAlgorithm
 
FHT3D() - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Description of the Method
FHTImage3D - Class in mcib3d.image3d.legacy
Deprecated.
FHTImage3D(ImageStack) - Constructor for class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Constructor for the FHTImage3D object the transform is automatically launched
FHTImage3D(ImageStack, boolean) - Constructor for class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Constructor for the FHTImage3D object
FHTImage3D(ImageProcessor) - Constructor for class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Constructor for the FHTImage3D object
FHTImage3D(ImageProcessor, boolean) - Constructor for class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Constructor for the FHTImage3D object
FHTImage3D(int, int, int, boolean) - Constructor for class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Constructor for the FHTImage3D object
fill(double, int, int) - Method in class mcib3d.image3d.ImageByte
 
fill(double, int, int) - Method in class mcib3d.image3d.ImageFloat
 
fill(double) - Method in class mcib3d.image3d.ImageHandler
 
fill(double, int, int) - Method in class mcib3d.image3d.ImageHandler
 
fill(double, int, int) - Method in class mcib3d.image3d.ImageShort
 
FILL - Static variable in class mcib3d.image3d.processing.FastOperation3D
 
fill(int) - Method in class mcib_plugins.Filter3D.Kernel3D
 
fill3D(FHTImage3D[], Vector3D[]) - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Fill 3D Reconstruction using central section theorem
FILL_AVG - Static variable in class mcib3d.align.Align2D
Description of the Field
Fill_Holes3D - Class in mcib_plugins
 
Fill_Holes3D() - Constructor for class mcib_plugins.Fill_Holes3D
 
FILL_NOISE - Static variable in class mcib3d.align.Align2D
Description of the Field
FILL_NONE - Static variable in class mcib3d.align.Align2D
Description of the Field
fillHoles3D(int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Fill holes for a binary image
FillHoles3D - Class in mcib3d.image3d.processing
/** Copyright (C) 2012 Jean Ollion This file is part of tango tango is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
FillHoles3D() - Constructor for class mcib3d.image3d.processing.FillHoles3D
 
fillMatrix(int) - Method in class mcib_plugins.Filter3D.Kernel3D
 
fillRange(int, int, int) - Method in class mcib3d.utils.ArrayUtil
 
fillValue(double) - Method in class mcib3d.utils.ArrayUtil
 
filter() - Method in class mcib_plugins.Filter3D.Filter3Ddefault
 
Filter3Ddefault - Class in mcib_plugins.Filter3D
default filter class walks through the image in 'snakewise' order and uses previous values for calculating the succeeding ones note: this was written for the mean filter and adapted for other filters a lot of code and comments have been kept to improve understanding the calculate_border_xx methods are very similar, they could have been combined but this would have made the code even more difficult to read rl vs rl use a different check against the borders rl vs tb vs fb 'walk' along different axes
Filter3Ddefault(ImageStack, ImageStack, int) - Constructor for class mcib_plugins.Filter3D.Filter3Ddefault
 
Filter3Ddefault.Voxel_value - Class in mcib_plugins.Filter3D
 
Filter3Dmax - Class in mcib_plugins.Filter3D
3D max
Filter3Dmax(ImageStack, ImageStack, int) - Constructor for class mcib_plugins.Filter3D.Filter3Dmax
 
Filter3DmaxLocal - Class in mcib_plugins.Filter3D
3D max
Filter3DmaxLocal(ImageStack, ImageStack, int) - Constructor for class mcib_plugins.Filter3D.Filter3DmaxLocal
 
Filter3Dmean - Class in mcib_plugins.Filter3D
3D mean
Filter3Dmean(ImageStack, ImageStack, int) - Constructor for class mcib_plugins.Filter3D.Filter3Dmean
 
Filter3Dmin - Class in mcib_plugins.Filter3D
3D min
Filter3Dmin(ImageStack, ImageStack, int) - Constructor for class mcib_plugins.Filter3D.Filter3Dmin
 
filter_mask_array - Variable in class mcib_plugins.Filter3D.Kernel3D
 
filter_size - Variable in class mcib_plugins.Filter3D.Kernel3D
 
filterFloatImage(ImageFloat, int, float, float, float, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
filterFloatImage(ImageFloat, int, Object3DVoxels, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
filterFloatImageStack(ImageStack, int, float, float, float, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
filterGeneric(ImageFloat, float, float, float, int, int, int) - Method in class mcib3d.image3d.ImageFloat
3D filter using threads
filterGeneric(ImageFloat, float, float, float, int, int, int, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageFloat
3D filter using threads
filterGeneric(ImageFloat, Object3DVoxels, int, int, int) - Method in class mcib3d.image3d.ImageFloat
 
filterGeneric(ImageFloat, Object3DVoxels, int, int, int, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageFloat
 
filterGeneric(ImageInt, float, float, float, int, int, int) - Method in class mcib3d.image3d.ImageInt
3D filter using threads
filterGeneric(ImageInt, float, float, float, int, int, int, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageInt
3D filter using threads
filterGeneric(ImageInt, Object3DVoxels, int, int, int) - Method in class mcib3d.image3d.ImageInt
 
filterGeneric(ImageInt, Object3DVoxels, int, int, int, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageInt
 
filterGeneric(IntImage3D, float, float, float, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
3D filter using threads
filterGeneric(RealImage3D, float, float, float, int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
3D filter using threads
filterImage(ImageHandler, int, float, float, float, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
filterImage(ImageHandler, int, Object3DVoxels, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
filterImageStack(ImageStack, int, float, float, float, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
filterIntImage(ImageInt, int, float, float, float, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
filterIntImage(ImageInt, int, float, float, float, int, boolean, AbstractLog) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
filterIntImage(ImageInt, int, Object3DVoxels, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
filterIntImageStack(ImageStack, int, float, float, float, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
filterPooling(ImageInt, int, int, int, int, int, int, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageInt
 
filterPooling(ImageInt, int, int, int, int, int) - Method in class mcib3d.image3d.ImageInt
 
Filters3d_jni - Class in mcib_plugins
3D filtering
Filters3d_jni() - Constructor for class mcib_plugins.Filters3d_jni
 
firstVoxelValueInt(int) - Method in class mcib3d.image3d.ImageInt
 
fitGaussian(double[], double, int) - Static method in class mcib3d.utils.ArrayUtil
Fit a gaussian to the values (radial distribution)
FLOAT - Static variable in class mcib3d.image3d.legacy.Image3D
Deprecated.
FLOAT
flood3D(IntImage3D, int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
Flood3D - Class in mcib3d.image3d.processing
* /** Copyright (C) 2012 Jean Ollion
Flood3D() - Constructor for class mcib3d.image3d.processing.Flood3D
 
flood3d26(ImageInt, int, int, int, int) - Static method in class mcib3d.image3d.processing.Flood3D
 
flood3d6(ImageInt, int, int, int, int) - Static method in class mcib3d.image3d.processing.Flood3D
 
flood3DNoise(ImageHandler, IntCoord3D, int, int) - Static method in class mcib3d.image3d.processing.Flood3D
 
flood3DNoise26Short(ImageShort, IntCoord3D, int, int) - Static method in class mcib3d.image3d.processing.Flood3D
 
flush() - Method in class mcib3d.image3d.ImageHandler
 
flushPixels() - Method in class mcib3d.image3d.ImageByte
 
flushPixels() - Method in class mcib3d.image3d.ImageFloat
 
flushPixels() - Method in class mcib3d.image3d.ImageHandler
 
flushPixels() - Method in class mcib3d.image3d.ImageShort
 
fromArrayListDouble(ArrayList<Double>) - Method in class mcib3d.utils.ArrayUtil
 
fromArrayListInt(ArrayList<Integer>) - Method in class mcib3d.utils.ArrayUtil
 
FRONT - Static variable in class mcib_plugins.Filter3D.Kernel3D
 
fusion(ImageLabeller.Spot3D) - Method in class mcib3d.image3d.ImageLabeller.Spot3D
 
fusion(ImageLabeller2D.Spot2D) - Method in class mcib3d.image3d.ImageLabeller2D.Spot2D
 

G

G_Border - Class in mcib3d.spatial.descriptors
 
G_Border() - Constructor for class mcib3d.spatial.descriptors.G_Border
 
G_Function - Class in mcib3d.spatial.descriptors
 
G_Function() - Constructor for class mcib3d.spatial.descriptors.G_Function
 
gaussianFit(int, int, int, boolean) - Method in class mcib3d.image3d.Segment3DSpots
 
GeomTransform3D - Class in mcib3d.geom
 
GeomTransform3D() - Constructor for class mcib3d.geom.GeomTransform3D
Constructor for the Transform3D object create an identity transform
GeomTransform3D(double[][]) - Constructor for class mcib3d.geom.GeomTransform3D
Constructor for the Transform3D object create an identity transform
GeomTransform3D(ArrayUtil) - Constructor for class mcib3d.geom.GeomTransform3D
Constructor for the GeomTransform3D object
GeomTransform3D(double, double, double, double, double, double) - Constructor for class mcib3d.geom.GeomTransform3D
Constructor for the GeomTranform3D object
get(int, int) - Method in class mcib3d.Jama.Matrix
Get a single element.
get(String) - Method in class mcib3d.utils.Message
Description of the Method
getA() - Method in class mcib3d.geom.MereoObject3D
 
getAddAngles() - Method in class mcib3d.ext.ImodConf
Gets the addAngles attribute of the ImodConf object
getAdjTriangles() - Method in class mcib3d.geom.deformation3d.Vertex
 
getAdjVertices(Vertex) - Method in class mcib3d.geom.deformation3d.Mesh
 
getAllColocalisationPairs() - Method in class mcib3d.geom.Objects3DPopulationColocalisation
Returns all the colocalisations
getAllDescendantsToEnd() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
getAllIndices() - Method in class mcib3d.geom.Objects3DPopulation
 
getAllRegionsAssociations() - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
getAlpha() - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getAlpha() - Method in class mcib3d.image3d.processing.CannyDeriche1D
 
getAlpha() - Method in class mcib3d.image3d.processing.CannyEdge3D
 
getAncestor() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
getAngle(int, int, int) - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the angle of the FHTImage3D pixel
getAngleDebut() - Method in class mcib3d.ext.ImodConf
Gets the angleDebut attribute of the ImodConf object
getAngleDebut() - Method in class mcib3d.ext.XmippConf
Gets the angleDebut attribute of the XmippConf object
getAngleFin() - Method in class mcib3d.ext.XmippConf
Gets the angleFin attribute of the XmippConf object
GetAngleFromAlign(int, String) - Method in class mcib3d.ext.Imod
Lit le fichier align.log pour extraire l'axe de tilt calcul� *
GetAngleFromAlign(int) - Method in class mcib3d.ext.Imod
Description of the Method
getAngleIncrement() - Method in class mcib3d.ext.ImodConf
Gets the angleIncrement attribute of the ImodConf object
getAngleIncrement() - Method in class mcib3d.ext.XmippConf
Gets the angleIncrement attribute of the XmippConf object
getAreaPixels() - Method in class mcib3d.geom.Object3D
the area of the Object3D (in pixels)
getAreaPixelsCorrected() - Method in class mcib3d.geom.Object3DVoxels
 
getAreaUnit() - Method in class mcib3d.geom.Object3D
Gets the areaUnit attribute of the Object3D object
getArray() - Method in class mcib3d.geom.Point3D
 
getArray() - Method in class mcib3d.Jama.Matrix
Access the internal two-dimensional array.
getArray() - Method in class mcib3d.utils.ArrayUtil
Gets the array attribute of the ArrayUtil object
getArray1D() - Method in class mcib3d.image3d.BlankMask
 
getArray1D() - Method in class mcib3d.image3d.ImageByte
 
getArray1D(int) - Method in class mcib3d.image3d.ImageByte
 
getArray1D() - Method in class mcib3d.image3d.ImageFloat
 
getArray1D(int) - Method in class mcib3d.image3d.ImageFloat
 
getArray1D() - Method in class mcib3d.image3d.ImageHandler
 
getArray1D(int) - Method in class mcib3d.image3d.ImageHandler
 
getArray1D() - Method in class mcib3d.image3d.ImageShort
get the 1D array as java Object
getArray1D(int) - Method in class mcib3d.image3d.ImageShort
get the 1D array as java Object for one slice
getArray1DByte(ImagePlus) - Static method in class mcib3d.image3d.ImageByte
 
getArray1DFloat(ImagePlus) - Static method in class mcib3d.image3d.ImageFloat
 
getArray1DShort(ImagePlus) - Static method in class mcib3d.image3d.ImageShort
(Should be somewhere else --> ImageJUtils ?) Get the 1D array of a 3D image stored in ImagePlus
getArrayCopy() - Method in class mcib3d.Jama.Matrix
Copy the internal two-dimensional array.
getArrayInt() - Method in class mcib3d.utils.ArrayUtil
 
getArrayList() - Method in class mcib3d.Classification.Attributes
 
getArrayList() - Method in class mcib3d.utils.ArrayUtil
 
getArrayValues(ImageHandler) - Method in class mcib3d.geom.Object3D
Gets the list of values inside an image as an array
getASM() - Method in class mcib_plugins.analysis.GLCMTexture
 
getAsso() - Method in class mcib3d.tracking_dev.AssociationPair
 
getAssociated(Object3D) - Method in class mcib3d.tracking_dev.Association
 
getAssociation(int) - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
getAssociationAsList() - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
getAssociationPairs() - Method in class mcib3d.tracking_dev.Association
 
getAssociations() - Method in class mcib3d.tracking_dev.Association
 
getAssociations() - Method in class mcib3d.tracking_dev.HungarianAlgorithm
 
getAssociationsAsIntegers() - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
getAssociationsAsString() - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
getAssociationTable() - Method in class mcib3d.tracking_dev.Association
Deprecated.
getAttribute(String) - Method in class mcib3d.Classification.Attributes
 
getB() - Method in class mcib3d.geom.MereoObject3D
 
getBille() - Method in class mcib3d.ext.ImodConf
Gets the bille attribute of the ImodConf object
getBinaryData() - Method in class mcib3d.image3d.ImageHandler
 
getBins() - Method in class mcib3d.utils.HistogramUtil
 
getBordersMerge(ArrayList<Integer>, boolean) - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
getBordersMerge(int[], boolean) - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
getBoundingBox() - Method in class mcib3d.geom.Object3D
Get the bounding box of the object (Xmin, Xmax, Ymin, Ymax, Zmin, Zmax)
getBoundingOriented() - Method in class mcib3d.geom.Object3D
 
getBounds(boolean) - Method in class mcib3d.image3d.BlankMask
 
getBounds(boolean) - Method in class mcib3d.image3d.ImageHandler
 
getCalibration() - Method in class mcib3d.geom.Object3D
Deprecated.
use Object3D-IJUtils Gets the calibration of the Object3D (ImageJ)
getCalibration(Object3D) - Static method in class mcib3d.geom.Object3D_IJUtils
 
getCalibration() - Method in class mcib3d.geom.ObjectCreator3D
Gets the calibration attribute of the Object3D object
getCalibration() - Method in class mcib3d.geom.Objects3DPopulation
Deprecated.
getCalibration() - Method in class mcib3d.image3d.ImageHandler
Deprecated.
getCannyDeriche() - Method in class mcib3d.image3d.processing.CannyDeriche1D
 
getCenterAsArray() - Method in class mcib3d.geom.Object3D
 
getCenterAsPoint() - Method in class mcib3d.geom.Object3D
Gets the center attribute of the Object3D object
getCenterAsVector() - Method in class mcib3d.geom.Object3D
Gets the center attribute of the Object3D object
getCenterAsVectorUnit() - Method in class mcib3d.geom.Object3D
Gets the center attribute of the Object3D object
getCenterFace(int) - Method in class mcib3d.geom.Object3DSurface
 
getCenterUnit() - Method in class mcib3d.geom.Object3D
Gets the centerUnit attribute of the Object3D object
getCenterX() - Method in class mcib3d.geom.Object3D
x coordinate of the center
getCenterX() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the centerX attribute of the Image3D object
getCenterY() - Method in class mcib3d.geom.Object3D
y coordinate of the center
getCenterY() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the centerY attribute of the Image3D object
getCenterZ() - Method in class mcib3d.geom.Object3D
z coordinate of the center
getCenterZ() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the centerZ attribute of the Image3D object
getChildren() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
getClassAttribute() - Method in class mcib3d.Classification.Attributes
 
getClassesProbability(Data) - Method in class mcib3d.Classification.Classifier
 
getClassIndex() - Method in class mcib3d.Classification.Attributes
 
getClosedObject(float, float, float) - Method in class mcib3d.geom.Object3D
 
getClusters() - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
getClustersArray() - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
getColoc(Object3D) - Method in class mcib3d.geom.Object3D
 
getColoc(Object3D) - Method in class mcib3d.geom.Object3DLabel
 
getColoc(Object3D) - Method in class mcib3d.geom.Object3DSurface
 
getColoc(Object3D) - Method in class mcib3d.geom.Object3DVoxels
 
getColocMitosis() - Method in class mcib3d.tracking_dev.Mitosis
 
getColocObject(Object3D, Object3D) - Method in class mcib3d.geom.Objects3DPopulationColocalisation
Return the colocalisation between two objects
getColocObject(int, int) - Method in class mcib3d.geom.Objects3DPopulationColocalisation
Return the colocalisation between two objects
getColocRaw(int, int) - Method in class mcib3d.geom.Objects3DPopulationColocalisation
Return the colocalisation between two indices (not necessarily objects values)
getColocVoxels(Object3D) - Method in class mcib3d.geom.Object3DVoxels
 
getColor(String) - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
recupere une couleur donnee a l'image3D
getColumn(int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
int donne une ligne de l'image3D
getColumnClass(int) - Method in class mcib_plugins.tools.ResultsTableModel
 
getColumnCount() - Method in class mcib_plugins.tools.ResultsTableModel
 
getColumnDimension() - Method in class mcib3d.Jama.Matrix
Get column dimension.
getColumnName(int) - Method in class mcib_plugins.tools.ResultsTableModel
 
getColumnPackedCopy() - Method in class mcib3d.Jama.Matrix
Make a one-dimensional column packed copy of the internal array.
getComment() - Method in class mcib3d.geom.Object3D
 
getCompactness(boolean) - Method in class mcib3d.geom.Object3D
Gets the compactness attribute of the Object3D (unit) related to sphericity
getCompactness() - Method in class mcib3d.geom.Object3D
 
getCompactnessCorrected() - Method in class mcib3d.geom.Object3DVoxels
 
getComposante(Vector3D) - Method in class mcib3d.geom.Vector3D
 
getConf() - Method in class mcib3d.ext.Imod
Gets the conf attribute of the Imod object
getConnexComponents() - Method in class mcib3d.geom.Object3DVoxels
 
getContours() - Method in class mcib3d.geom.Object3D
return the list of contour voxels
getContours() - Method in class mcib3d.geom.Object3DFuzzy
 
getContrast() - Method in class mcib_plugins.analysis.GLCMTexture
 
getConvexObject(boolean) - Method in class mcib3d.geom.Object3D
 
getConvexObject() - Method in class mcib3d.geom.Object3D
 
getConvexPolygonRoi(int) - Method in class mcib3d.geom.Object3D
 
getConvexSurface() - Method in class mcib3d.geom.Object3D
 
getCopy() - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
getCopy() - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
getCopy() - Method in class mcib3d.utils.ArrayUtil
Gets the copy of the ArrayUtil object
getCorrelation() - Method in class mcib_plugins.analysis.GLCMTexture
 
getCount(int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the count attribute of the IntImage3D object
getCumulNumber(int) - Method in class mcib3d.utils.HistogramUtil
 
getCumulNumbers() - Method in class mcib3d.utils.HistogramUtil
 
getCurrentObject() - Method in class mcib3d.geom.ObjectsPopulationDistances
 
getCurvatureFaces(double[]) - Method in class mcib3d.geom.Object3DSurface
 
getCurvatureGaussBonnet(int) - Method in class mcib3d.geom.Object3DSurface
 
getCurvatures(int) - Method in class mcib3d.geom.Object3DSurface
 
getCurvaturesGaussBonnet() - Method in class mcib3d.geom.Object3DSurface
 
getCurvatureTangent(int, int) - Method in class mcib3d.geom.Object3DSurface
 
getD() - Method in class mcib3d.Jama.EigenvalueDecomposition
Return the block diagonal eigenvalue matrix
getDamImage() - Method in class mcib3d.image3d.regionGrowing.Watershed3D
 
getDamValue() - Method in class mcib3d.image3d.regionGrowing.Watershed3D
 
getData() - Method in class mcib3d.Classification.Data
 
getDaughter1() - Method in class mcib3d.tracking_dev.Mitosis
 
getDaughter2() - Method in class mcib3d.tracking_dev.Mitosis
 
getDifferenceNext() - Method in class mcib3d.utils.ArrayUtil
 
getDifferenceNextAbs() - Method in class mcib3d.utils.ArrayUtil
 
getDilatedObject(float, float, float) - Method in class mcib3d.geom.Object3D
 
getDiscreteCompactness() - Method in class mcib3d.geom.Object3DVoxels
 
getDistanceMap(float, float, float, boolean, int) - Method in class mcib3d.image3d.ImageHandler
 
getDistanceMapInsideMask(int) - Method in class mcib3d.image3d.ImageInt
 
getDistBB() - Method in class mcib3d.geom.ObjectDistBB
 
getDistCenterMax() - Method in class mcib3d.geom.Object3D
the maximum distance between center and contours
getDistCenterMaxPixel() - Method in class mcib3d.geom.Object3D
the maximum distance between center and contours
getDistCenterMean() - Method in class mcib3d.geom.Object3D
the average distance between center and contours
getDistCenterMeanPixel() - Method in class mcib3d.geom.Object3D
the average distance between center and contours
getDistCenterMin() - Method in class mcib3d.geom.Object3D
the minimum distance between center and contours
getDistCenterMinPixel() - Method in class mcib3d.geom.Object3D
the minimum distance between center and contours
getDistCenterSigma() - Method in class mcib3d.geom.Object3D
the sigma value for distances between center and contours
getDistCenterSigmaPixel() - Method in class mcib3d.geom.Object3D
the sigma value for distances between center and contours
getDistMax() - Method in class mcib3d.tracking_dev.CostColocalisation
 
getDoublePivot() - Method in class mcib3d.Jama.LUDecomposition
Return pivot permutation vector as a one-dimensional double array
getEdge() - Method in class mcib3d.image3d.processing.CannyEdge3D
 
getEdges() - Method in class mcib3d.image3d.processing.SymmetryFilter
 
getEllipsoid() - Method in class mcib3d.geom.Object3D
 
getEllipsoid() - Method in class mcib3d.geom.RDAR
 
getEntropy() - Method in class mcib_plugins.analysis.GLCMTexture
 
getEraser() - Method in class mcib3d.ext.ImodConf
Gets the eraser attribute of the ImodConf object
getErodedObject(float, float, float) - Method in class mcib3d.geom.Object3D
 
getExclure() - Method in class mcib3d.ext.ImodConf
Gets the exclure attribute of the ImodConf object
getExtensionFunctions() - Method in class mcib_plugins.tools.RoiManager3D_2
Gets the extensionFunctions attribute of the RoiManager3D_ object
getFacesNormals() - Method in class mcib3d.geom.deformation3d.Mesh
 
getFeret() - Method in class mcib3d.geom.Object3D
Gets the feret diameter of the object (unit)
getFeretVoxel1() - Method in class mcib3d.geom.Object3D
Gets the first feret voxel of the object (unit)
getFeretVoxel2() - Method in class mcib3d.geom.Object3D
Gets the second feret voxel of the object (unit)
getFiles(String) - Method in class mcib3d.geom.deformation3d.IO
 
getFinalAssociation() - Method in class mcib3d.tracking_dev.MitosisDetector
 
getFirst() - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
getFirstLocalExtrema(double, double) - Method in class mcib3d.utils.ArrayUtil
 
getFirstLocalMaxima(int, double) - Method in class mcib3d.utils.ArrayUtil
 
getFirstLocalMinima(double) - Method in class mcib3d.utils.ArrayUtil
 
getFirstVoxel() - Method in class mcib3d.geom.Object3DVoxels
 
getFloatMaximum() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the maximum pixel value
getFloatMinimum() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the minimum pixel value
getFrame() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
getFullInfo(int) - Method in class mcib3d.utils.Chrono
 
getFuzzyObjects(float, ImageFloat) - Method in class mcib3d.geom.Object3DFactory
Deprecated.
 
getGeometricInvariants() - Method in class mcib3d.geom.Object3D
Compute geometric invariants, based on orders 4 moments refer to Xu and Li 2008.
getGlobalScaling() - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getGradient(double, double, double) - Method in class mcib3d.geom.GradientPoint
 
getGradientsXYZ() - Method in class mcib3d.image3d.processing.CannyEdge3D
 
getH() - Method in class mcib3d.Jama.QRDecomposition
Return the Householder vectors
getHisto(ImageInt) - Method in class mcib3d.image3d.BlankMask
 
getHisto(ImageInt, int, double, double) - Method in class mcib3d.image3d.BlankMask
 
getHisto(ImageInt) - Method in class mcib3d.image3d.ImageByte
 
getHisto(ImageInt, int, double, double) - Method in class mcib3d.image3d.ImageByte
 
getHisto(ImageInt) - Method in class mcib3d.image3d.ImageFloat
 
getHisto(ImageInt, int, double, double) - Method in class mcib3d.image3d.ImageFloat
 
getHisto(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getHisto(ImageInt, int, double, double) - Method in class mcib3d.image3d.ImageHandler
 
getHisto(ImageInt) - Method in class mcib3d.image3d.ImageShort
 
getHisto(ImageInt, int, double, double) - Method in class mcib3d.image3d.ImageShort
 
getHisto256() - Method in class mcib3d.image3d.ImageStats
 
getHisto256BinSize() - Method in class mcib3d.image3d.ImageStats
 
getHistogram(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getHistogram() - Method in class mcib3d.image3d.ImageHandler
 
getHistogram(ImageInt, int, double, double) - Method in class mcib3d.image3d.ImageHandler
 
getHistogram(ArrayList<? extends Point3D>, int, double, double) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
getHistogram(LinkedList<? extends Point3D>, int, double, double) - Method in class mcib3d.image3d.ImageHandler
 
getHistogram() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
compute the histogram of the image
getHistogram() - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
donne l'histogramme de l'image3D 16 bits
getHistogram() - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
donne l'histogramme de l'image3D 32 bits en decoupage de 65 536 bins // attention pas de lien direct entre case et valeur pixel
getHistogram(int) - Method in class mcib3d.utils.ArrayUtil
 
getHomogeneousInvariants() - Method in class mcib3d.geom.Object3D
Compute homogeneous invariants, based on orders 4 moments
getHyperStack(String, ImageHandler[]) - Static method in class mcib3d.image3d.ImageHandler
 
getICQ() - Method in class mcib3d.image3d.processing.ImageColocalizer
 
getId() - Method in class mcib3d.geom.deformation3d.Vertex
 
getIDM() - Method in class mcib_plugins.analysis.GLCMTexture
 
getImag(int, int, int) - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the imag attribute of the FHTImage3D object
getImage(int, boolean) - Method in class mcib3d.align.Align2D
Gets the image attribute of the Align2D object
getImage(int, boolean, int) - Method in class mcib3d.align.Align2D
Gets the image attribute of the Align2D object
getImage(int) - Method in class mcib3d.align.Align2D
Gets the image attribute of the Align2D object
getImage(int) - Method in class mcib3d.align.Align3D
Gets the image attribute of the Align3D object
getImage() - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getImage() - Method in class mcib3d.image3d.ImageStats
 
getImageHandler() - Method in class mcib3d.geom.ObjectCreator3D
Gets the image3D attribute of the ObjectCreator3D object
getImagEigenvalues() - Method in class mcib3d.Jama.EigenvalueDecomposition
Return the imaginary parts of the eigenvalues
getImagePeaks() - Method in class mcib3d.image3d.processing.MaximaFinder
Do the computation and returns the result
getImagePlus() - Method in class mcib3d.image3d.BlankMask
 
getImagePlus(byte[], int, int, int, boolean) - Static method in class mcib3d.image3d.ImageByte
 
getImagePlus(float[], int, int, int, boolean) - Static method in class mcib3d.image3d.ImageFloat
 
getImagePlus(int[], int, int, int, boolean) - Static method in class mcib3d.image3d.ImageFloat
 
getImagePlus() - Method in class mcib3d.image3d.ImageHandler
 
getImagePlus(short[], int, int, int, boolean) - Static method in class mcib3d.image3d.ImageShort
(Should be somewhere else --> ImageJUtils ?) Get the ImagePlus from a 1D array of pixels
getImageStack() - Method in class mcib3d.image3d.ImageHandler
 
getImageStats(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getImageTransformedMultiThread(ImageHandler, GeomTransform3D) - Static method in class mcib3d.geom.GeomTransform3D
 
getIndexFromName(String) - Method in class mcib3d.geom.Objects3DPopulation
 
getIndexFromValue(int) - Method in class mcib3d.geom.Objects3DPopulation
 
getIndexOf(Object3D) - Method in class mcib3d.geom.Objects3DPopulation
 
getInput() - Method in class mcib3d.image3d.processing.CannyEdge3D
 
getInStack(ImageStack, boolean, int) - Method in class mcib3d.align.Align2D
gets the images on which the alignment is performed in the given stack
the images could be with or without alignement beware there is always a duplication of the images (even if not applying alignment)
getInstances() - Method in class mcib3d.Classification.DataSet
 
getIntegerHistogram() - Method in class mcib3d.utils.ArrayUtil
 
getIntegratedDensity(ImageHandler) - Method in class mcib3d.geom.Object3D
integrated density of the Object3D in an image
getIntegratedDensity(ImageHandler, ImageHandler) - Method in class mcib3d.geom.Object3D
 
getInteractions() - Method in class mcib3d.tracking_dev.CostPairMitosis
 
getInterior3DFill() - Method in class mcib3d.geom.Object3DVoxels
 
getIntermediates() - Method in class mcib3d.image3d.processing.SymmetryFilter
 
getInternalLabelImage() - Method in class mcib3d.image3d.Segment3DSpots
 
getInterObject() - Method in class mcib3d.geom.MereoObject3D
 
getIntersectionBox(Object3D) - Method in class mcib3d.geom.Object3D
 
getIntersectionObject(Object3D) - Method in class mcib3d.geom.Object3D
Get the intersection voxels as a 3D object
getInverseCumulNumbers() - Method in class mcib3d.utils.HistogramUtil
 
getIteration() - Method in class mcib3d.ext.XmippConf
Gets the iteration attribute of the XmippConf object
getKurtosis() - Method in class mcib3d.utils.ArrayUtil
Kurtosis, order 4
getL() - Method in class mcib3d.Jama.CholeskyDecomposition
Return triangular factor.
getL() - Method in class mcib3d.Jama.LUDecomposition
Return lower triangular factor
getLabel() - Method in class mcib3d.geom.Voxel3DComparable
 
getLabelImage() - Method in class mcib3d.geom.Object3D
Gets the label image of the object (should start at 0,0
getLabelImage() - Method in class mcib3d.image3d.Segment3DSpots
 
getLabelledObjectsImage3D() - Method in class mcib3d.image3d.Segment3DImage
 
getLabelledObjectsStack() - Method in class mcib3d.image3d.Segment3DImage
 
getLabels(ImageHandler, boolean) - Method in class mcib3d.image3d.ImageLabeller
 
getLabels(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller
 
getLabels(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller2D
 
getLabelsFloat(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller
 
getLabelsFloat(ImageHandler, boolean) - Method in class mcib3d.image3d.ImageLabeller
 
getLabelsFloat(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller2D
 
getLabelsFloat(ImageHandler, boolean) - Method in class mcib3d.image3d.ImageLabeller2D
 
getLabelsIndividualVoxels(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller
 
getLabelsIndividualVoxelsFloat(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller
 
getLastAlpha() - Method in class mcib3d.geom.Gradient
 
getLayerEVFObject(ImageInt, float) - Method in class mcib3d.geom.Object3D
 
getLayerEVFObject(Object3D, float) - Method in class mcib3d.geom.Object3D
 
getLayerObject(float, float) - Method in class mcib3d.geom.Object3D
 
getLength() - Method in class mcib3d.geom.Vector3D
Gets the value attribute of the Pixel3D object
getLength(double, double) - Method in class mcib3d.geom.Vector3D
Gets the length attribute of the Vector3D object with units
getLengthSquare() - Method in class mcib3d.geom.Vector3D
 
getLengthSquare(double, double) - Method in class mcib3d.geom.Vector3D
 
getLimitInf(int) - Method in class mcib3d.utils.ArrayUtil
First encoutered value not zero, starting from th
getLimitSup() - Method in class mcib3d.utils.ArrayUtil
Last index whose value is not zero
getLine() - Method in class mcib3d.geom.deformation3d.Deriche
 
getLine() - Method in class mcib3d.image3d.processing.CannyDeriche1D
 
getLineageTo(ObjectTrack) - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
getLinearPixelAt(double, double, double) - Method in class mcib3d.geom.Gradient
 
getLinePixelValue(int, int, int, int, int, int, boolean) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
 
getLinePixelValue(Point3D, Vector3D, double, double, boolean) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
 
getLineX(int, int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getLineY(int, int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getLineZ(int, int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getList() - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
getListAssociation() - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
getListLabel() - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
getListMaxima(float, float, float, int, int) - Method in class mcib3d.image3d.ImageFloat
 
getListMaxima(float, float, float, int, int, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageFloat
 
getListMaxima(float, float, float, int, int) - Method in class mcib3d.image3d.ImageInt
 
getListMaxima(float, float, float, int, int, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageInt
 
getListMaxima(ImageHandler, float, float, float, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
getListMaximaFloat(ImageFloat, float, float, float, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
getListMaximaInt(ImageInt, float, float, float, int, boolean) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
getListPeaks() - Method in class mcib3d.image3d.processing.MaximaFinder
 
getLocalMaximum(int, int, int, float, float, float) - Method in class mcib3d.image3d.Segment3DSpots
 
getLocalThreshold() - Method in class mcib3d.image3d.Segment3DSpots
 
getLog() - Method in class mcib3d.geom.Objects3DPopulation
 
getLog() - Method in class mcib3d.utils.Logger.TextLog
 
getMainAxis() - Method in class mcib3d.geom.deformation3d.Mesh
 
getMainAxis() - Method in class mcib3d.geom.Object3D
Gets the mainAxis attribute of the Object3D object (unit)
getMainElongation() - Method in class mcib3d.geom.Object3D
Gets the main elongation of the object
getMap() - Method in class mcib3d.geom.interactions.InteractionsList
Deprecated.
getMask() - Method in class mcib3d.geom.Objects3DPopulation
 
getMask() - Method in class mcib3d.image3d.ImageStats
 
getMask() - Method in class mcib3d.spatial.sampler.SpatialRandom
 
getMask() - Method in class mcib3d.spatial.sampler.SpatialRandomHardCore
 
getMassCenterX(ImageHandler) - Method in class mcib3d.geom.Object3D
x coordinate of the center of mass in an image
getMassCenterY(ImageHandler) - Method in class mcib3d.geom.Object3D
u coordinate of the center of mass in an image
getMassCenterZ(ImageHandler) - Method in class mcib3d.geom.Object3D
z coordinate of the center of mass in an image
getMatrix() - Method in class mcib3d.geom.GeomTransform3D
Gets the matrix attribute of the GeomTransform3D object
getMatrix(int, int, int, int) - Method in class mcib3d.Jama.Matrix
Get a submatrix.
getMatrix(int[], int[]) - Method in class mcib3d.Jama.Matrix
Get a submatrix.
getMatrix(int, int, int[]) - Method in class mcib3d.Jama.Matrix
Get a submatrix.
getMatrix(int[], int, int) - Method in class mcib3d.Jama.Matrix
Get a submatrix.
getMatrixAxes() - Method in class mcib3d.geom.Object3D
Gets the main axes vectors as a matrix
getMax() - Method in class mcib3d.geom.Voxel3DComparable
 
getMax(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getMax() - Method in class mcib3d.image3d.ImageHandler
Get the maximum value in the image
getMax() - Method in class mcib3d.image3d.ImageStats
 
getMax() - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
getMax2() - Method in class mcib3d.geom.Voxel3DComparable
 
getMaxAbsDifference(ArrayUtil) - Method in class mcib3d.utils.ArrayUtil
 
getMaxBelowValue(float) - Method in class mcib3d.image3d.ImageHandler
 
getMaxCorrelation(ImageProcessor, ImageProcessor) - Static method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the maxCorrelation attribute of the FHTImage3D class
getMaxCorrelation(ImageStack, ImageStack) - Static method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the maxCorrelation attribute of the FHTImage3D class
getMaxCorrelation(Image3D, Image3D, int, int, int) - Static method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the maxCorrelation attribute of the FHTImage3D class
getMaxCorrelation(ImageStack, ImageStack, int, int, int) - Static method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the maxCorrelation attribute of the FHTImage3D class
getMaxCorrelation(ImageProcessor, ImageProcessor, int, int) - Static method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the maxCorrelation attribute of the FHTImage3D class
getMaxCost() - Method in class mcib3d.tracking_dev.CostPairMitosis
 
getMaxCost() - Method in class mcib3d.tracking_dev.CostTouching
 
getMaxDistance() - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getMaximum() - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
donne le maximum de l'image3D
getMaximum() - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
donne le maximum de l'image3D
getMaximum() - Method in class mcib3d.utils.ArrayUtil
The maximum value
getMaximumAbove(double) - Method in class mcib3d.utils.ArrayUtil
The maximum value
getMaximumBelow(double) - Method in class mcib3d.utils.ArrayUtil
 
getMaximumIndex() - Method in class mcib3d.utils.ArrayUtil
The maximum value
getMaximumStarting(int) - Method in class mcib3d.utils.ArrayUtil
 
getMaxLabelImage(int) - Method in class mcib3d.geom.Object3D
Get the label image starting at 0,0,0
getMaxPixel() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the maxPixel attribute of the Image3D object
getMaxPosition() - Method in class mcib3d.image3d.ImageHandler
Return the position of the voxel having maximum value in the image
getMaxsize() - Method in class mcib3d.image3d.ImageLabeller
 
getMaxsize() - Method in class mcib3d.image3d.ImageLabeller2D
 
getMaxSizeAllObjects() - Method in class mcib3d.geom.Objects3DPopulation
 
getMaxSizeObject() - Method in class mcib3d.image3d.Segment3DImage
 
getMean(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getMean() - Method in class mcib3d.image3d.ImageHandler
 
getMean() - Method in class mcib3d.image3d.ImageStats
 
getMean() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the mean Value of the Image3D
getMean(int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the meanValue attribute of the IntImage3D object
getMean() - Method in class mcib3d.utils.ArrayUtil
Average value
getMeanCurvatureVertexFaces(double[]) - Method in class mcib3d.geom.Object3DSurface
 
getMeanPixValueAroundBarycenter(boolean, ImageInt, ImageHandler, double, double) - Method in class mcib3d.geom.Object3D
 
getMeasure(int) - Method in class mcib3d.geom.Object3D
Utility to perform measurement
getMeasureCentroid() - Method in class mcib3d.geom.Objects3DPopulation
 
getMeasuresBase() - Method in class mcib_plugins.analysis.simpleMeasure
 
getMeasuresCentroid() - Method in class mcib_plugins.analysis.simpleMeasure
 
getMeasuresGeometrical() - Method in class mcib3d.geom.Objects3DPopulation
 
getMeasuresMesh() - Method in class mcib3d.geom.Objects3DPopulation
Deprecated.
getMeasuresShape() - Method in class mcib3d.geom.Objects3DPopulation
 
getMeasuresShape() - Method in class mcib_plugins.analysis.simpleMeasure
 
getMeasuresStats(ImageHandler) - Method in class mcib3d.geom.Objects3DPopulation
 
getMeasuresStats(ImageStack) - Method in class mcib3d.geom.Objects3DPopulation
 
getMeasuresStats(ImageHandler) - Method in class mcib_plugins.analysis.simpleMeasure
 
getMeasuresStats(ImagePlus) - Method in class mcib_plugins.analysis.simpleMeasure
 
getMedianElongation() - Method in class mcib3d.geom.Object3D
Gets the flatness of the object
getMeshSurfaces() - Method in class mcib_plugins.analysis.simpleMeasure
 
getMin(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getMin() - Method in class mcib3d.image3d.ImageHandler
 
getMin() - Method in class mcib3d.image3d.ImageStats
 
getMinAboveValue(float) - Method in class mcib3d.image3d.ImageHandler
Gets the minAboveValue attribute of the FishImage3D object
getMinAboveValue(int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the minAboveValue attribute of the FishImage3D object
getMinAndMax(ImageInt) - Method in class mcib3d.image3d.BlankMask
 
getMinAndMax(ImageInt) - Method in class mcib3d.image3d.ImageByte
 
getMinAndMax(ImageInt) - Method in class mcib3d.image3d.ImageFloat
 
getMinAndMax(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getMinAndMax(ImageInt) - Method in class mcib3d.image3d.ImageShort
 
getMinAndMaxArray(ArrayList<? extends Point3D>) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
getMinAndMaxArray(LinkedList<? extends Point3D>) - Method in class mcib3d.image3d.ImageHandler
 
getMinColoc() - Method in class mcib3d.tracking_dev.CostPairMitosis
 
getMinColocMitosis() - Method in class mcib3d.tracking_dev.MitosisDetector
 
getMinimum() - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
donne le minimum de l'image3D
getMinimum() - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
donne le minimum de l'image3D
getMinimum() - Method in class mcib3d.utils.ArrayUtil
The minimum value
getMinimumAbove(double) - Method in class mcib3d.utils.ArrayUtil
Gets the minimum value above a threshold
getMinimumIndex() - Method in class mcib3d.utils.ArrayUtil
 
getMinMax() - Method in class mcib3d.utils.ArrayUtil
 
getMinSize() - Method in class mcib3d.image3d.ImageLabeller
 
getMinSize() - Method in class mcib3d.image3d.ImageLabeller2D
 
getMinSizeObject() - Method in class mcib3d.image3d.Segment3DImage
 
getMode() - Method in class mcib3d.utils.ArrayUtil
 
getModel() - Method in class mcib_plugins.tools.ResultsFrame
 
getModeNonZero() - Method in class mcib3d.utils.ArrayUtil
 
getMoments(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getMoments3D() - Method in class mcib3d.geom.Object3D
This code is taken from the BIOCAT platform: http://faculty.cs.niu.edu/~zhou/tool/biocat/ Reference for BIOCAT: J.
getMomentsRaw2() - Method in class mcib3d.geom.Object3D
Returns the moments order 2
getMomentsRaw3() - Method in class mcib3d.geom.Object3D
Returns the moments order 3
getMomentsRaw4() - Method in class mcib3d.geom.Object3D
Returns the moments order 4
getMother() - Method in class mcib3d.tracking_dev.Mitosis
 
getName() - Method in class mcib3d.geom.Object3D
The name of the object
getName() - Method in class mcib3d.spatial.descriptors.F_Function
 
getName() - Method in class mcib3d.spatial.descriptors.G_Border
 
getName() - Method in class mcib3d.spatial.descriptors.G_Function
 
getName() - Method in class mcib3d.spatial.descriptors.H_Border
 
getName() - Method in class mcib3d.spatial.descriptors.H_Function
 
getName() - Method in class mcib3d.spatial.descriptors.K_Function
 
getName() - Method in interface mcib3d.spatial.descriptors.SpatialDescriptor
 
getName() - Method in interface mcib3d.spatial.sampler.SpatialModel
 
getName() - Method in class mcib3d.spatial.sampler.SpatialRandom
 
getName() - Method in class mcib3d.spatial.sampler.SpatialRandomHardCore
 
getName() - Method in class mcib3d.spatial.sampler.SpatialShuffle
 
getNbBins() - Method in class mcib3d.utils.HistogramUtil
 
getNbChildren() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
getNbClusters() - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
getNbColor() - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Gets the nbColor attribute of the ColorImage3D object
getNbCpus() - Static method in class mcib3d.utils.ThreadUtil
 
getNbFromKernel(int[]) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
getNbLabels() - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
getNbMoments3D() - Static method in class mcib3d.geom.Object3D
 
getNbObj() - Method in class mcib3d.image3d.Segment3DImage
 
getNbObjects() - Method in class mcib3d.geom.Objects3DPopulation
 
getNbObjectsinSizeRange(ImageHandler, boolean) - Method in class mcib3d.image3d.ImageLabeller
 
getNbObjectsinSizeRange(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller
 
getNbObjectsInSizeRange(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller2D
 
getNbObjectsTotal(ImageHandler, boolean) - Method in class mcib3d.image3d.ImageLabeller
 
getNbObjectsTotal(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller
 
getNbObjectsTotal(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller2D
 
getNbPixel() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
 
getNbUniqueVertices() - Method in class mcib3d.geom.Object3DSurface
 
getNearestNeighbor(double[], int) - Method in class mcib3d.utils.KDTreeC
Gets the N nearest neighbors to the given key.
getNeighborhood(int, int, int, float, float, float) - Method in class mcib3d.image3d.ImageHandler
Gets the neighboring of a pixel (default=sphere)
getNeighborhood(int, int, int, float, float, float) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the neighboring of a pixel (default=sphere)
getNeighborhood(Image3D, int, int, int) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the neighboring of a pixel, with a kernel as an image
getNeighborhood3x3x3(int, int, int) - Method in class mcib3d.image3d.ImageHandler
Gets the 3D neighborhood of the pixel in 8 connexion --> 27 pixels
getNeighborhood3x3x3(int, int, int) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the 3D neighborhood of the pixel in 8 connexion --> 27 pixels
getNeighborhood3x3x3CenterList(int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getNeighborhood3x3x3ListCenter(int, int, int) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
getNeighborhood3x3x3ListNoCenter(int, int, int) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
getNeighborhood3x3x3NoCenterList(int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getNeighborhoodBrick(int, int, int, int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getNeighborhoodCross3D(int, int, int) - Method in class mcib3d.image3d.ImageHandler
6-neighborhood in 3D cross of a given voxel
getNeighborhoodCross3D(int, int, int) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
 
getNeighborhoodCross3DList(int, int, int, boolean) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
getNeighborhoodGrayKernelAdd(IntImage3D, int, int, int) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
 
getNeighborhoodGrayKernelMinus(IntImage3D, int, int, int) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
 
getNeighborhoodKernel(int[], int, int, int, int, float, float, float) - Method in class mcib3d.image3d.ImageHandler
Gets the neighboring attribute of the Image3D with a kernel as a array
getNeighborhoodKernel(Object3D, int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getNeighborhoodKernel(int[], int, int, int, int, float, float, float) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the neighboring attribute of the Image3D with a kernel as a array
getNeighborhoodKernelAdd(Object3D, ImageHandler, int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getNeighborhoodKernelSubstract(Object3D, ImageHandler, int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getNeighborhoodLayer(int, int, int, float, float) - Method in class mcib3d.image3d.ImageHandler
Get the neighborhood as a layer of pixels
getNeighborhoodLayer(int, int, int, float, float, ImageHandler) - Method in class mcib3d.image3d.ImageHandler
Get the neighborhood as a layer of pixels
getNeighborhoodLayer(int, int, int, float, float, IntImage3D) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Get the neighborhood as a layer of pixels
getNeighborhoodLayer(int, int, int, float, float) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Get the neighborhood as a layer of pixels
getNeighborhoodLayerAngle(int, int, int, float, float, double, Vector3D) - Method in class mcib3d.image3d.ImageHandler
Get the neighborhood as a layer of pixels
getNeighborhoodLayerList(int, int, int, float, float) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
getNeighborhoodLayerList(int, int, int, float, float, ImageInt) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
getNeighborhoodSphere(int, int, int, float, float, float) - Method in class mcib3d.image3d.ImageHandler
Gets the neighboring of a pixel (sphere)
getNeighborhoodSphere(int, int, int, float, float, float) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the neighboring of a pixel (sphere)
getNeighborhoodSphere(int, int, int, float, float, float, RealImage3D) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the neighboring of a pixel (sphere)
getNeighborhoodXY3x3(int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getNeighborVertices(int) - Method in class mcib3d.geom.Object3DSurface
 
getNomSerie() - Method in class mcib3d.ext.ImodConf
Gets the nomSerie attribute of the ImodConf object
getNomSerie() - Method in class mcib3d.ext.XmippConf
Gets the nomSerie attribute of the XmippConf object
getNonLabelledVoxels(int, boolean) - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
 
getNorm(int, int, int) - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the norm of the FHTImage3D pixel
getNormalFace(int) - Method in class mcib3d.geom.Object3DSurface
 
getNormalizedVector() - Method in class mcib3d.geom.Vector3D
 
getNormalVertex(int) - Method in class mcib3d.geom.Object3DSurface
 
getNormalVertexWeighted(int) - Method in class mcib3d.geom.Object3DSurface
 
getNotAssociatiated1() - Method in class mcib3d.tracking_dev.HungarianAlgorithm
 
getNotAssociatiated2() - Method in class mcib3d.tracking_dev.HungarianAlgorithm
 
getNumber(int) - Method in class mcib3d.utils.HistogramUtil
 
getNumbering(ImageHandler) - Method in class mcib3d.geom.Object3D
Will count the number of different objects within this object *
getObject(int) - Method in class mcib3d.geom.Objects3DPopulation
 
getObject1ColocalisationPairs(Object3D) - Method in class mcib3d.geom.Objects3DPopulationColocalisation
Returns all the colocalisations for one specific object in population 1
getObject1ColocalisationPairs(Object3D) - Method in class mcib_plugins.Interactions_
 
getObject2ColocalisationPairs(Object3D) - Method in class mcib3d.geom.Objects3DPopulationColocalisation
Returns all the colocalisations for one specific object in population 2
getObject2ColocalisationPairs(Object3D) - Method in class mcib3d.geom.Objects3DPopulationInteractions
 
getObject2ColocalisationPairs(Object3D) - Method in class mcib_plugins.Interactions_
 
getObject3D() - Method in class mcib3d.geom.ObjectDistBB
 
getObject3D() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
getObject3D1() - Method in class mcib3d.geom.PairColocalisation
 
getObject3D1() - Method in class mcib3d.tracking_dev.AssociationPair
 
getObject3D1fromAsso(String) - Method in class mcib3d.tracking_dev.Association
 
getObject3D2() - Method in class mcib3d.geom.PairColocalisation
 
getObject3D2() - Method in class mcib3d.tracking_dev.AssociationPair
 
getObject3D2fromAsso(String) - Method in class mcib3d.tracking_dev.Association
 
getObject3DBackground(ImageInt) - Method in class mcib3d.image3d.ImageInt
 
getObject3DSurface() - Method in class mcib3d.geom.Object3D
Convert the object to surface (if necessary)
getObject3DVoxels() - Method in class mcib3d.geom.Object3D
Convert the object to voxels (if necessary)
getObject3DVoxels(int) - Method in class mcib3d.geom.ObjectCreator3D
 
getObjectByName(String) - Method in class mcib3d.geom.Objects3DPopulation
 
getObjectByValue(int) - Method in class mcib3d.geom.Objects3DPopulation
 
getObjectIndex(int) - Method in class mcib3d.geom.Objects3DPopulation
 
getObjectMask() - Method in class mcib3d.image3d.ImageInt
 
getObjects(boolean) - Method in class mcib3d.geom.Object3DFactory
Deprecated.
 
getObjects(ImageHandler, boolean) - Method in class mcib3d.image3d.ImageLabeller
 
getObjects(ImageHandler) - Method in class mcib3d.image3d.ImageLabeller
 
getObjects() - Method in class mcib3d.image3d.processing.ManualSpot
 
getObjects() - Method in class mcib3d.image3d.Segment3DSpots
 
getObjects3D(ImageFloat, float) - Method in class mcib3d.image3d.ImageInt
Deprecated.
getObjects3D() - Method in class mcib3d.image3d.ImageInt
 
getObjects3DPopulation() - Method in class mcib3d.image3d.ImageInt
 
getObjectsArray() - Method in class mcib3d.geom.Objects3DPopulation
 
getObjectsList() - Method in class mcib3d.geom.Objects3DPopulation
 
getObjectsRelation(int, int, String) - Method in class mcib3d.geom.MereoAnalysis
 
getObjectsWithinDistanceBorder(Object3D, double) - Method in class mcib3d.geom.Objects3DPopulation
 
getObjectsWithinDistanceCenter(Object3D, double) - Method in class mcib3d.geom.Objects3DPopulation
 
getObjectsWithinVolume(double, double, boolean) - Method in class mcib3d.geom.Objects3DPopulation
 
getOpenedObject(float, float, float) - Method in class mcib3d.geom.Object3D
 
getOrientedScaling(Vector3D) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getOrphan1() - Method in class mcib3d.tracking_dev.Association
 
getOrphan1Population() - Method in class mcib3d.tracking_dev.Association
 
getOrphan2() - Method in class mcib3d.tracking_dev.Association
 
getOrphan2Population() - Method in class mcib3d.tracking_dev.Association
 
getPair(int, int) - Method in class mcib3d.geom.interactions.InteractionsList
 
getParent() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
getPart(int, int, int) - Method in class mcib3d.align.Align2D
Gets the part attribute of the Align2D object
getPartsIn() - Method in class mcib3d.geom.RDAR
 
getPartsIn(int) - Method in class mcib3d.geom.RDAR
 
getPartsInNumber() - Method in class mcib3d.geom.RDAR
 
getPartsInNumber(int) - Method in class mcib3d.geom.RDAR
 
getPartsInVolumePixels() - Method in class mcib3d.geom.RDAR
 
getPartsInVolumePixels(int) - Method in class mcib3d.geom.RDAR
 
getPartsInVolumeUnit() - Method in class mcib3d.geom.RDAR
 
getPartsInVolumeUnit(int) - Method in class mcib3d.geom.RDAR
 
getPartsOut() - Method in class mcib3d.geom.RDAR
 
getPartsOut(int) - Method in class mcib3d.geom.RDAR
 
getPartsOutNumber() - Method in class mcib3d.geom.RDAR
 
getPartsOutNumber(int) - Method in class mcib3d.geom.RDAR
 
getPartsOutVolumePixels() - Method in class mcib3d.geom.RDAR
 
getPartsOutVolumePixels(int) - Method in class mcib3d.geom.RDAR
 
getPartsOutVolumeUnit() - Method in class mcib3d.geom.RDAR
 
getPartsOutVolumeUnit(int) - Method in class mcib3d.geom.RDAR
 
getPathedImage() - Method in class mcib3d.tracking_dev.TrackingAssociation
 
getPearson() - Method in class mcib3d.image3d.processing.ImageColocalizer
 
getPercentile(double, ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getPivot() - Method in class mcib3d.Jama.LUDecomposition
Return pivot permutation vector
getPix(int, int, int) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the voxel value of the Image3D object
getPix(float, float, float) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the voxel value of the Image3D object (interpolated value)
getPix(Voxel3D, boolean) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
 
getPix(int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the pix attribute of the IntImage3D object
getPix(float, float, float) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the pix attribute of the IntImage3D object
getPix(Voxel3D, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
getPix(int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Gets the pixel value at position (x,y,z) as a double
getPix(float, float, float) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Gets the trilinear interpolated pixel value at position (x,y,z) as a double
getPix(Voxel3D, boolean) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
 
getPixCenterValue(ImageHandler) - Method in class mcib3d.geom.Object3D
 
getPixel(int) - Method in class mcib3d.image3d.BlankMask
 
getPixel(int, int, int) - Method in class mcib3d.image3d.BlankMask
 
getPixel(int, int) - Method in class mcib3d.image3d.BlankMask
 
getPixel(IntCoord3D) - Method in class mcib3d.image3d.BlankMask
 
getPixel(int, int) - Method in class mcib3d.image3d.ImageByte
 
getPixel(int) - Method in class mcib3d.image3d.ImageByte
Deprecated.
getPixel(Voxel3D, boolean) - Method in class mcib3d.image3d.ImageByte
 
getPixel(int, int, int) - Method in class mcib3d.image3d.ImageByte
 
getPixel(IntCoord3D) - Method in class mcib3d.image3d.ImageByte
 
getPixel(Point3D) - Method in class mcib3d.image3d.ImageByte
 
getPixel(Point3DInt) - Method in class mcib3d.image3d.ImageByte
 
getPixel(int) - Method in class mcib3d.image3d.ImageFloat
Deprecated.
getPixel(IntCoord3D) - Method in class mcib3d.image3d.ImageFloat
 
getPixel(Coordinate3D) - Method in class mcib3d.image3d.ImageFloat
 
getPixel(int, int, int) - Method in class mcib3d.image3d.ImageFloat
 
getPixel(int, int) - Method in class mcib3d.image3d.ImageFloat
 
getPixel(Point3D) - Method in class mcib3d.image3d.ImageFloat
 
getPixel(Point3DInt) - Method in class mcib3d.image3d.ImageFloat
 
getPixel(int) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
getPixel(int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
getPixel(int, int) - Method in class mcib3d.image3d.ImageHandler
 
getPixel(Point3D) - Method in class mcib3d.image3d.ImageHandler
 
getPixel(Point3DInt) - Method in class mcib3d.image3d.ImageHandler
 
getPixel(float, float, float) - Method in class mcib3d.image3d.ImageHandler
 
getPixel(float, float, float, ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getPixel(Point3D) - Method in class mcib3d.image3d.ImageInt
 
getPixel(int) - Method in class mcib3d.image3d.ImageShort
Deprecated.
getPixel(Point3D) - Method in class mcib3d.image3d.ImageShort
 
getPixel(Point3DInt) - Method in class mcib3d.image3d.ImageShort
 
getPixel(int, int, int) - Method in class mcib3d.image3d.ImageShort
 
getPixel(int, int) - Method in class mcib3d.image3d.ImageShort
 
getPixel(int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
recupere la valeur du pixel de coordonnees (x,y,z)
getPixel(Point3D, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the pixel attribute of the IntImage3D object
getPixel(Voxel3D, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the pixel attribute of the IntImage3D object
getPixel(Vector3D, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the pixel attribute of the IntImage3D object
getPixel(float, float, float) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the pixel attribute of the IntImage3D object with tri-linear interpolation
getPixel(double, double, double) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
getPixel(int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Gets the pixel value at position (x,y,z)
getPixel(float, float, float) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Gets the trilinear interpolated pixel value at position (x,y,z)
getPixel(double, double, double) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
 
getPixelBorder(double, double, double) - Method in class mcib3d.geom.Object3D
 
getPixelInt(int, int) - Method in class mcib3d.image3d.BlankMask
 
getPixelInt(int, int, int) - Method in class mcib3d.image3d.BlankMask
 
getPixelInt(int) - Method in class mcib3d.image3d.BlankMask
 
getPixelInt(int, int) - Method in class mcib3d.image3d.ImageByte
 
getPixelInt(int) - Method in class mcib3d.image3d.ImageByte
Deprecated.
getPixelInt(int, int, int) - Method in class mcib3d.image3d.ImageByte
 
getPixelInt(IntCoord3D) - Method in class mcib3d.image3d.ImageByte
 
getPixelInt(Point3D) - Method in class mcib3d.image3d.ImageByte
 
getPixelInt(int, int) - Method in class mcib3d.image3d.ImageInt
 
getPixelInt(int, int, int) - Method in class mcib3d.image3d.ImageInt
 
getPixelInt(int) - Method in class mcib3d.image3d.ImageInt
Deprecated.
getPixelInt(Point3D) - Method in class mcib3d.image3d.ImageInt
 
getPixelInt(Point3D) - Method in class mcib3d.image3d.ImageShort
 
getPixelInt(int, int, int) - Method in class mcib3d.image3d.ImageShort
 
getPixelInt(int, int) - Method in class mcib3d.image3d.ImageShort
 
getPixelInt(int) - Method in class mcib3d.image3d.ImageShort
Deprecated.
getPixelInterpolated(Point3D) - Method in class mcib3d.image3d.ImageByte
 
getPixelInterpolated(Point3D) - Method in class mcib3d.image3d.ImageFloat
 
getPixelInterpolated(Point3D) - Method in class mcib3d.image3d.ImageHandler
 
getPixelInterpolated(Point3D) - Method in class mcib3d.image3d.ImageInt
 
getPixelInterpolated(Point3D) - Method in class mcib3d.image3d.ImageShort
 
getPixelIntInterpolated(Point3D) - Method in class mcib3d.image3d.ImageByte
 
getPixelIntInterpolated(Point3D) - Method in class mcib3d.image3d.ImageInt
 
getPixelIntInterpolated(Point3D) - Method in class mcib3d.image3d.ImageShort
 
getPixelMax(ImageHandler) - Method in class mcib3d.geom.Object3D
compute the voxel with maximum value in an image
getPixelMax(ImageHandler) - Method in class mcib3d.geom.Object3DFuzzy
 
getPixelMax(ImageHandler) - Method in class mcib3d.geom.Object3DLabel
 
getPixelMax(ImageHandler) - Method in class mcib3d.geom.Object3DSurface
 
getPixelMax(ImageHandler) - Method in class mcib3d.geom.Object3DVoxels
 
getPixelMin(ImageHandler) - Method in class mcib3d.geom.Object3DFuzzy
 
getPixelMoments(int, int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the pixelMoments attribute of the IntImage3D object
getPixelTransformedI(Voxel3D, GeomTransform3D) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Gets the pixel corresponding to the direct application of the transform given
getPixelTransformedI(double, double, double, GeomTransform3D) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Gets the pixel corresponding to the direct application of the transform given
getPixelValue(int, int, int) - Method in class mcib3d.align.Align2D
Gets the pixelValue attribute of the Align2D object
getPixMaxValue(ImageHandler) - Method in class mcib3d.geom.Object3D
Gets the pixMaxValue attribute of the Object3D object
getPixMeanValue(ImageHandler) - Method in class mcib3d.geom.Object3D
Gets the meanPixValue attribute of the Object3D object
getPixMeanValueContour(ImageHandler) - Method in class mcib3d.geom.Object3D
 
getPixMedianValue(ImageHandler) - Method in class mcib3d.geom.Object3D
 
getPixMedianValue(ImageHandler) - Method in class mcib3d.geom.Object3DVoxels
 
getPixMinValue(ImageHandler) - Method in class mcib3d.geom.Object3D
Gets the pixMinValue attribute of the Object3D object
getPixModeNonZero(ImageHandler) - Method in class mcib3d.geom.Object3D
 
getPixModeValue(ImageHandler) - Method in class mcib3d.geom.Object3D
 
getPixStdDevValue(ImageHandler) - Method in class mcib3d.geom.Object3D
Gets the SD of pixels in object
getPlot() - Method in class mcib3d.spatial.analysis.SpatialStatistics
 
getPlot() - Method in class mcib3d.utils.ArrayUtil
 
getPlot(String, String, String) - Method in class mcib3d.utils.ArrayUtil
 
getPlus() - Method in class mcib3d.geom.ObjectCreator3D
 
getPlus() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
 
getPoint3f() - Method in class mcib3d.geom.Point3D
 
getPopA() - Method in class mcib3d.geom.MereoAnalysis
 
getPopB() - Method in class mcib3d.geom.MereoAnalysis
 
getPopulation() - Method in class mcib3d.geom.ObjectsPopulationDistances
 
getPosition() - Method in class mcib3d.geom.deformation3d.Vertex
 
getPosition() - Method in class mcib3d.geom.Point3D
Gets the position attribute of the Point3D object
getPotentialMother(ImageHandler) - Method in class mcib3d.tracking_dev.Mitosis
 
getPow2Img() - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Gets the pow2Img attribute of the RealImage3D object
getPow2Img(int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Gets the pow2Img attribute of the RealImage3D object
getPowerSpectrum() - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the powerSpectrum attribute of the FHTImage3D object
getPowerSpectrum(boolean) - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the powerStack attribute of the FHTImage3D object
getProf(int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
donne une ligne en Z dans l'image 3D
getQ() - Method in class mcib3d.Jama.QRDecomposition
Generate and return the (economy-sized) orthogonal factor
getQuantilePixValue(ImageHandler, double) - Method in class mcib3d.geom.Object3D
Gets the quantile value of the object in the image
getR() - Method in class mcib3d.Jama.QRDecomposition
Return the upper triangular factor
getRadialPixelAt(double, double, double) - Method in class mcib3d.geom.Gradient
Get the pixel value at ???
getRadiiFromObject(Object3D) - Static method in class mcib3d.image3d.processing.FastFilters3D
 
getRadius() - Method in class mcib3d.image3d.processing.SymmetryFilter
 
getRadiusMoments(int) - Method in class mcib3d.geom.Object3D
 
getRadX() - Method in class mcib3d.geom.MereoAnalysis
 
getRadX() - Method in class mcib3d.geom.MereoObject3D
 
getRadY() - Method in class mcib3d.geom.MereoAnalysis
 
getRadY() - Method in class mcib3d.geom.MereoObject3D
 
getRadZ() - Method in class mcib3d.geom.MereoAnalysis
 
getRadZ() - Method in class mcib3d.geom.MereoObject3D
 
getRandomPerpendicularVector() - Method in class mcib3d.geom.Vector3D
 
getRandomPointInMask() - Method in class mcib3d.geom.Objects3DPopulation
 
getRandomSample() - Method in class mcib_plugins.analysis.spatialAnalysis
 
getRandomVoxel(Random) - Method in class mcib3d.geom.Object3DVoxels
Get a random voxel in the object
getRandomvoxel(Random) - Method in class mcib3d.geom.Object3DVoxels
Deprecated.
getRange(double[], double[]) - Method in class mcib3d.utils.KDTreeC
Returns all PointKD within a certain range defined by an upper and lower PointKD.
getRatioBox() - Method in class mcib3d.geom.Object3D
Gets the ration between volume and volume of the bounding box (in units)
getRatioEllipsoid() - Method in class mcib3d.geom.Object3D
Gets the ration between volume and volume of the ellipsoid (in units)
getRawImage() - Method in class mcib3d.image3d.regionGrowing.Watershed3D
Get the raw image used
getRawImage() - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
Get the raw image used
getRawImage() - Method in class mcib3d.image3d.Segment3DSpots
 
getRCC8Relationship() - Method in class mcib3d.geom.MereoObject3D
 
getReal(int, int, int) - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the real attribute of the FHTImage3D object
getRealEigenvalues() - Method in class mcib3d.Jama.EigenvalueDecomposition
Return the real parts of the eigenvalues
getRec() - Method in class mcib3d.ext.XmippConf
Gets the rec attribute of the XmippConf object
getRegion(int) - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
getRelationships() - Method in class mcib3d.geom.MereoAnalysis
 
getRepertoireTmp() - Method in class mcib3d.ext.Imod
Gets the repertoireTmp attribute of the Imod object
getResult(int, int) - Method in class mcib3d.geom.MereoAnalysis
 
getResults(boolean) - Method in class mcib3d.geom.MereoAnalysis
 
getResultsTable(boolean, boolean) - Method in class mcib3d.geom.MereoAnalysis
 
getResultsTableAll(boolean) - Method in class mcib3d.geom.Objects3DPopulationColocalisation
get the results of colocalisation as an ImageJ Results Table
getResultsTableAssociation() - Method in class mcib3d.tracking_dev.TrackingAssociation
 
getResultsTableInteractions(boolean) - Method in class mcib3d.geom.Objects3DPopulationInteractions
 
getResultsTableMitosis() - Method in class mcib3d.tracking_dev.TrackingAssociation
 
getResultsTableOnlyColoc(boolean) - Method in class mcib3d.geom.Objects3DPopulationColocalisation
 
getResultsTableOnlyColoc(boolean) - Method in class mcib_plugins.Interactions_
 
getResXY() - Method in class mcib3d.geom.Object3D
Gets the calibration in XY of the Object3D
getResZ() - Method in class mcib3d.geom.Object3D
Gets the calibration in Z of the Object3D
getRoi() - Method in class mcib3d.align.Align2D
Gets the roi attribute of the Align2D object
getRoot() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
getRootMeanSquare() - Method in class mcib3d.image3d.ImageStats
 
getRotated(Vector3D, double) - Method in class mcib3d.geom.Object3DSurface
 
getRotation(int) - Method in class mcib3d.align.Align2D
Gets the rotation attribute of the Align2D object
getRotationAxis() - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getRoundX() - Method in class mcib3d.geom.Point3D
 
getRoundY() - Method in class mcib3d.geom.Point3D
 
getRoundZ() - Method in class mcib3d.geom.Point3D
 
getRow(int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
donne une ligne de l'image3D
getRowCount() - Method in class mcib_plugins.tools.ResultsTableModel
 
getRowDimension() - Method in class mcib3d.Jama.Matrix
Get row dimension.
getRowPackedCopy() - Method in class mcib3d.Jama.Matrix
Make a one-dimensional row packed copy of the internal array.
getS() - Method in class mcib3d.Jama.SingularValueDecomposition
Return the diagonal matrix of singular values
getSample() - Method in interface mcib3d.spatial.sampler.SpatialModel
 
getSample() - Method in class mcib3d.spatial.sampler.SpatialRandom
 
getSample() - Method in class mcib3d.spatial.sampler.SpatialRandomHardCore
 
getSample() - Method in class mcib3d.spatial.sampler.SpatialShuffle
 
getSampleImage() - Method in interface mcib3d.spatial.sampler.SpatialModel
 
getSampleImage() - Method in class mcib3d.spatial.sampler.SpatialRandom
 
getSampleImage() - Method in class mcib3d.spatial.sampler.SpatialRandomHardCore
 
getSampleImage() - Method in class mcib3d.spatial.sampler.SpatialShuffle
 
getScaleXY() - Method in class mcib3d.geom.Objects3DPopulation
 
getScaleXY() - Method in class mcib3d.image3d.BlankMask
 
getScaleXY() - Method in class mcib3d.image3d.ImageHandler
 
getScaleZ() - Method in class mcib3d.geom.Objects3DPopulation
 
getScaleZ() - Method in class mcib3d.image3d.BlankMask
 
getScaleZ() - Method in class mcib3d.image3d.ImageHandler
 
getSdi() - Method in class mcib3d.spatial.analysis.SpatialStatistics
 
getSdi_F() - Method in class mcib_plugins.analysis.spatialAnalysis
 
getSdi_G() - Method in class mcib_plugins.analysis.spatialAnalysis
 
getSdi_H() - Method in class mcib_plugins.analysis.spatialAnalysis
 
getSeeds() - Method in class mcib3d.image3d.regionGrowing.Watershed3D
Get the seeds image used
getSeeds() - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
Get the seeds image used
getSeeds() - Method in class mcib3d.image3d.Segment3DSpots
 
getSeedsThreshold() - Method in class mcib3d.image3d.Segment3DSpots
 
getSeg() - Method in class mcib_plugins.segmentation.SegNuclei
 
getShiftY() - Method in class mcib3d.ext.ImodConf
Gets the shiftY attribute of the ImodConf object
getSigma() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the std dev value of the Image3D
getSigma(int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the sigma attribute of the IntImage3D object
getSingularValues() - Method in class mcib3d.Jama.SingularValueDecomposition
Return the one-dimensional array of singular values
getSize() - Method in class mcib3d.image3d.ImageLabeller.Spot3D
 
getSize() - Method in class mcib3d.image3d.ImageLabeller2D.Spot2D
 
getSize() - Method in class mcib3d.utils.ArrayUtil
Deprecated.
see size() get the number of elements
getSizeInMb() - Method in class mcib3d.image3d.ImageByte
 
getSizeInMb() - Method in class mcib3d.image3d.ImageFloat
 
getSizeInMb() - Method in class mcib3d.image3d.ImageHandler
 
getSizeInMb() - Method in class mcib3d.image3d.ImageShort
 
getSizex() - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Gets the sizex attribute of the ColorImage3D object
getSizex() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the sizex attribute of the Image3D object
getSizey() - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Gets the sizey attribute of the ColorImage3D object
getSizey() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the sizey attribute of the Image3D object
getSizez() - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Gets the sizez attribute of the ColorImage3D object
getSizez() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the sizez attribute of the Image3D object
getSkewness() - Method in class mcib3d.utils.ArrayUtil
skewness, order 3
getSmoothingFactor() - Method in class mcib3d.geom.Object3DSurface
 
getSmoothSurface() - Method in class mcib3d.geom.Object3DSurface
 
getSmoothSurfaceArea() - Method in class mcib3d.geom.Object3DSurface
 
getSmoothSurfaceAreaUnit() - Method in class mcib3d.geom.Object3DSurface
 
getSphericity() - Method in class mcib3d.geom.Object3D
 
getSphericity(boolean) - Method in class mcib3d.geom.Object3D
Gets the sphericity attribute of the Object3D (unit) related to compactness
getSphericityCorrected() - Method in class mcib3d.geom.Object3DVoxels
 
getStack(boolean, int) - Method in class mcib3d.align.Align2D
gets the images on which the alignment is performed
the images could be with or without alignement beware there is always a duplication of the images (even if not applying alignment)
getStack() - Method in class mcib3d.geom.deformation3d.Deriche
 
getStack() - Method in class mcib3d.geom.ObjectCreator3D
Returns an ImageStack
getStack() - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
recupere l'Image3D comme une ImageStack
getStack() - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the IJstack attribute of the FHTImage3D object
getStack() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Get the imageJ IJstack (for displaying)
getStack() - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Gets the ImageStack associated with the 3D image
getStack() - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Gets the IJstack attribute of the RealImage3D object
getStandardDeviation() - Method in class mcib3d.image3d.ImageStats
 
getState() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
getStatsForces() - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getStdDev() - Method in class mcib3d.utils.ArrayUtil
standard deviation
getSubClusters(int) - Method in class mcib3d.image3d.regionGrowing.Cluster
 
getSubListAssociation(ArrayList<Integer>) - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
getSubTabUtil(int, int) - Method in class mcib3d.utils.ArrayUtil
extract a sub-array from this array
getSum() - Method in class mcib3d.utils.ArrayUtil
sum of all elements
getSum() - Method in class mcib_plugins.analysis.GLCMTexture
 
getSumAbs() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the sum of absolute values of the Image3D
getSumAbsForces() - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getSurfaceMesh() - Method in class mcib3d.geom.Object3DSurface
 
getSurfaceMeshUnit() - Method in class mcib3d.geom.Object3DSurface
 
getSurfaceObjectsImage3D() - Method in class mcib3d.image3d.Segment3DImage
 
getSurfaceObjectsStack() - Method in class mcib3d.image3d.Segment3DImage
 
getSurfaceTriangles(boolean) - Method in class mcib3d.geom.Object3DSurface
 
getSurfaceTrianglesPixels(boolean) - Method in class mcib3d.geom.Object3DSurface
 
getSurfaceTrianglesUnit(boolean) - Method in class mcib3d.geom.Object3DSurface
 
getSymmetry(boolean) - Method in class mcib3d.image3d.processing.SymmetryFilter
 
getTailleX() - Method in class mcib3d.ext.XmippConf
Gets the tailleX attribute of the XmippConf object
getTailleY() - Method in class mcib3d.ext.XmippConf
Gets the tailleY attribute of the XmippConf object
getTangentVector(int, int) - Method in class mcib3d.geom.Object3DSurface
 
getThickness() - Method in class mcib3d.ext.ImodConf
Gets the thickness attribute of the ImodConf object
getThresholdMax() - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getThresholdMin() - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getThumbNail(int, int) - Method in class mcib3d.image3d.ImageHandler
 
getThumbNail(int, int, ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getThumbnailImage(int, int, int, int, ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
getTiltAngle() - Method in class mcib3d.ext.ImodConf
Gets the tiltAngle attribute of the ImodConf object
getTiltAxis() - Method in class mcib3d.ext.XmippConf
Gets the tiltAxis attribute of the XmippConf object
getTitle() - Method in class mcib3d.image3d.ImageHandler
 
getTrackedImage() - Method in class mcib3d.tracking_dev.TrackingAssociation
 
getTransform(int) - Method in class mcib3d.align.Align3D
Gets the transform attribute of the Align3D object
getTransformPixel(Voxel3D, GeomTransform3D) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Gets the pixel corresponding to the pixel given if the transform is applied (inversion of matrice)
getTranslation() - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
getTranslation(FHTImage3D, int, int, int) - Static method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the translation attribute of the FHTImage3D class
getTranslation(FHTImage3D) - Static method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the translation attribute of the FHTImage3D class
getTriangleList() - Method in class mcib3d.geom.deformation3d.Mesh
 
getTx(int) - Method in class mcib3d.align.Align2D
Gets the translation on X Axis for an image
getTy(int) - Method in class mcib3d.align.Align2D
Gets the translation on Y Axis for an image
getType() - Method in class mcib3d.geom.Object3D
The type
getType() - Method in class mcib3d.image3d.ImageByte
 
getType() - Method in class mcib3d.image3d.ImageFloat
 
getType() - Method in class mcib3d.image3d.ImageHandler
 
getType() - Method in class mcib3d.image3d.ImageShort
 
getType() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Gets the data type attribute of the Image3D object
getU() - Method in class mcib3d.Jama.LUDecomposition
Return upper triangular factor
getU() - Method in class mcib3d.Jama.SingularValueDecomposition
Return the left singular vectors
getUniqueValues(int) - Method in class mcib3d.image3d.ImageInt
 
getUniqueValues() - Method in class mcib3d.image3d.ImageInt
 
getUniqueVertex(int) - Method in class mcib3d.geom.Object3DSurface
 
getUniqueVertices() - Method in class mcib3d.geom.deformation3d.Mesh
 
getUniqueVerticesIndexes() - Method in class mcib3d.geom.Object3DSurface
 
getUnit() - Method in class mcib3d.geom.Objects3DPopulation
 
getUnit() - Method in class mcib3d.image3d.ImageHandler
 
getUnits() - Method in class mcib3d.geom.Object3D
Gets the unit attribute of the Object3D object
getUpdatedLabelsAsString() - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
getV() - Method in class mcib3d.Jama.EigenvalueDecomposition
Return the eigenvector matrix
getV() - Method in class mcib3d.Jama.SingularValueDecomposition
Return the right singular vectors
getValue(int, int) - Method in class mcib3d.geom.GeomTransform3D
Gets the value of the matrix of the Transform3D object at position [row][column]
getValue() - Method in class mcib3d.geom.Object3D
Value of the Object3D
getValue() - Method in class mcib3d.geom.Voxel3D
Gets the value attribute of the Voxel3D object
getValue(int, int, int) - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Gets the value attribute of the FHTImage3D object
getValue(int) - Method in class mcib3d.utils.ArrayUtil
get value at an index
getValue1FromAsso(String) - Static method in class mcib3d.tracking_dev.Association
 
getValue2FromAsso(String) - Static method in class mcib3d.tracking_dev.Association
 
getValueArray(ImageHandler) - Method in class mcib3d.geom.Object3DVoxels
 
getValueAt(int, int, int) - Method in class mcib_plugins.Filter3D.Kernel3D
 
getValueAt(int, int) - Method in class mcib_plugins.tools.ResultsTableModel
 
getValueAxis(int) - Method in class mcib3d.geom.Object3D
Gets the valueAxis attribute of the Object3D object (unit)
getValueInt(int) - Method in class mcib3d.utils.ArrayUtil
 
getValues(String) - Static method in class mcib3d.tracking_dev.Association
 
getVariance() - Method in class mcib3d.utils.ArrayUtil
Variance value (not biased)
getVariance2() - Method in class mcib3d.utils.ArrayUtil
Variance value (not biased) fast version
getVector3D() - Method in class mcib3d.geom.Point3D
Gets the vector3D attribute of the Point3D object
getVectorAxis(int) - Method in class mcib3d.geom.Object3D
Gets the Axis attribute of the Object3D object (unit)
getVectorTransformed(Vector3D, Vector3D) - Method in class mcib3d.geom.GeomTransform3D
Apply the transform to a point described by a vector
getVERSION() - Static method in class mcib3d.utils.AboutMCIB
 
getVertex(int) - Method in class mcib3d.geom.Object3DSurface
 
getVertexList() - Method in class mcib3d.geom.deformation3d.Mesh
 
getVertices() - Method in class mcib3d.geom.deformation3d.Triangle
 
getVerticesNormals() - Method in class mcib3d.geom.deformation3d.Mesh
 
getVois(ImageHandler) - Method in class mcib3d.image3d.Coordinate3D
 
getVois() - Method in class mcib3d.image3d.Coordinate3D
 
getVois(int) - Method in class mcib3d.image3d.MaskIterator
Deprecated.
 
getVois1() - Method in class mcib3d.image3d.Coordinate3D
 
getVois1(ImageHandler) - Method in class mcib3d.image3d.Coordinate3D
 
getVois1(int) - Method in class mcib3d.image3d.MaskIterator
Deprecated.
 
getVois15(ImageHandler) - Method in class mcib3d.image3d.Coordinate3D
 
getVois15() - Method in class mcib3d.image3d.Coordinate3D
 
getVois15(int) - Method in class mcib3d.image3d.MaskIterator
Deprecated.
 
getVois1C3D() - Method in class mcib3d.image3d.Coordinate3D
 
getVois1Vox() - Method in class mcib3d.image3d.Coordinate3D
 
getVolumeBoundingBoxOrientedPixel() - Method in class mcib3d.geom.Object3D
the volume of the oriented bounding box FIXME computing of oriented box
getVolumeBoundingBoxPixel() - Method in class mcib3d.geom.Object3D
the volume of the bounding box
getVolumeColoc() - Method in class mcib3d.geom.PairColocalisation
 
getVolumeEllipseUnit() - Method in class mcib3d.geom.Object3D
The volume of the approximated ellipsoid in unit the main radius is DCMax
getVolumeLabels() - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
getVolumeMax() - Method in class mcib3d.image3d.Segment3DSpots
 
getVolumeMergeLabels(int[], ArrayList<Voxel3D>) - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
getVolumeMergeLabels(ArrayList<Integer>, ArrayList<Voxel3D>) - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
getVolumeMin() - Method in class mcib3d.image3d.Segment3DSpots
 
getVolumePixels() - Method in class mcib3d.geom.Object3D
volume of the Object3D (in pixel)
getVolumeUnit() - Method in class mcib3d.geom.Object3D
Gets the volume of the Object3D in units
getVoronoiLines(boolean) - Method in class mcib3d.image3d.regionGrowing.Watershed3DVoronoi
 
getVoronoiZones(boolean) - Method in class mcib3d.image3d.regionGrowing.Watershed3DVoronoi
 
getVoxel(int, int, int) - Method in class mcib_plugins.Filter3D.Filter3Ddefault
 
getVoxelInsideBoundingBox(int[]) - Method in class mcib3d.geom.Object3DVoxels
 
getVoxels() - Method in class mcib3d.geom.Object3D
Get the list of voxels of the object
getVoxels() - Method in class mcib3d.geom.Object3DFuzzy
 
getVoxels() - Method in class mcib3d.geom.Object3DLabel
 
getVoxels() - Method in class mcib3d.geom.Object3DSurface
 
getVoxels() - Method in class mcib3d.geom.Object3DVoxels
 
getWatershedImage3D() - Method in class mcib3d.image3d.regionGrowing.Watershed3D
 
getWatershedImage3D(int) - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
compute the watershed image, only for voxels with value > threshold
getWatershedImage3D() - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
compute the watershed image
getWatershedImageStack(int) - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
compute the watershed image
getWatershedImageStack() - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
compute the watershed image
getX() - Method in class mcib3d.geom.Point3D
Get the value of x
getX() - Method in class mcib3d.geom.Point3DInt
 
getXmax() - Method in class mcib3d.geom.Object3D
Gets the xmax attribute of the Object3D
getXmin() - Method in class mcib3d.geom.Object3D
Gets the xmin attribute of the Object3D
getXYCoord(int) - Method in class mcib3d.geom.Voxel3D
 
getY() - Method in class mcib3d.geom.Point3D
Get the value of y
getY() - Method in class mcib3d.geom.Point3DInt
 
getYmax() - Method in class mcib3d.geom.Object3D
Gets the ymax attribute of the Object3D
getYmin() - Method in class mcib3d.geom.Object3D
Gets the ymin attribute of the Object3D
getYnumbers() - Method in class mcib3d.utils.HistogramUtil
 
getZ() - Method in class mcib3d.geom.Point3D
Get the value of z
getZ() - Method in class mcib3d.geom.Point3DInt
 
getZmax() - Method in class mcib3d.geom.Object3D
Gets the zmax attribute of the Object3D
getZmin() - Method in class mcib3d.geom.Object3D
Gets the zmin attribute of the Object3D
GLCMTexture - Class in mcib_plugins.analysis
 
GLCMTexture(ImagePlus, int, int) - Constructor for class mcib_plugins.analysis.GLCMTexture
 
Gradient - Class in mcib3d.geom
Copyright (C) Thomas Boudier License: This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
Gradient() - Constructor for class mcib3d.geom.Gradient
Constructeur de l'objet Gradient
Gradient(int[], double[], double[]) - Constructor for class mcib3d.geom.Gradient
Constructeur de l'objet Gradient
Gradient(int[], double[], double[], int) - Constructor for class mcib3d.geom.Gradient
Constructeur de l'objet Gradient
gradient(int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
The gradient of the image in a given direction (sobel)
GradientPoint - Class in mcib3d.geom
 
GradientPoint(double, double, double, double, double, double, double, boolean) - Constructor for class mcib3d.geom.GradientPoint
 
grayDilatation(IntImage3D) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
grayErosion(IntImage3D) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
grayReconstruction(IntImage3D) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
greedyMatch() - Method in class mcib3d.tracking_dev.HungarianAlgorithm
Find a valid matching by greedily selecting among zero-cost matchings.
GREEN - Variable in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Description of the Field

H

h - Variable in class mcib3d.image3d.distanceMap3d.CleanUpLocalThickness
Deprecated.
 
h - Variable in class mcib3d.image3d.distanceMap3d.DistanceRidge
Deprecated.
 
h - Variable in class mcib3d.image3d.distanceMap3d.LocalThickness
Deprecated.
 
H_Border - Class in mcib3d.spatial.descriptors
 
H_Border() - Constructor for class mcib3d.spatial.descriptors.H_Border
 
H_Function - Class in mcib3d.spatial.descriptors
 
H_Function() - Constructor for class mcib3d.spatial.descriptors.H_Function
 
handleExtension(String, Object[]) - Method in class mcib_plugins.tools.RoiManager3D_2
Description of the Method
hard(Image, double) - Method in class mcib_plugins.processing.Thresholder
Applies hard thresholding to an image.
hasBrothers() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
hashCode() - Method in class mcib3d.geom.Point3D
 
hashCode() - Method in class mcib3d.geom.Voxel3D
 
hashCode() - Method in class mcib3d.image3d.BlankMask
 
hashCode() - Method in class mcib3d.image3d.ImageLabeller.Vox3D
 
hashCode() - Method in class mcib3d.image3d.ImageLabeller2D.Vox2D
 
hashName - Variable in class mcib3d.geom.Objects3DPopulation
 
hashValue - Variable in class mcib3d.geom.Objects3DPopulation
 
hasNext() - Method in class mcib3d.image3d.Coordinate3D
 
hasObject(Object3D) - Method in class mcib3d.tracking_dev.Mitosis
 
hasOneValue(float) - Method in class mcib3d.image3d.ImageHandler
 
hasOneValue(ArrayList) - Method in class mcib3d.utils.ArrayUtil
One of the values are in the array ?
hasOneValueInt(int) - Method in class mcib3d.image3d.ImageInt
 
hasOneValueInt(ArrayList) - Method in class mcib3d.utils.ArrayUtil
One of the values are in the array ? For int values (does not work if ArrayList is int and values is double)
hasOneVoxelColoc(Object3D) - Method in class mcib3d.geom.Object3D
 
hasOneVoxelColoc(Object3D) - Method in class mcib3d.geom.Object3DLabel
 
hasOneVoxelColoc(Object3D) - Method in class mcib3d.geom.Object3DSurface
 
hasOneVoxelColoc(Object3D) - Method in class mcib3d.geom.Object3DVoxels
 
hasOneVoxelValueRange(ImageHandler, int, int) - Method in class mcib3d.geom.Object3D
 
hasOneVoxelValueRange(ImageHandler, int, int) - Method in class mcib3d.geom.Object3DLabel
 
hasOneVoxelValueRange(ImageHandler, int, int) - Method in class mcib3d.geom.Object3DSurface
 
hasOneVoxelValueRange(ImageHandler, int, int) - Method in class mcib3d.geom.Object3DVoxels
 
hasOnlyValue(int) - Method in class mcib3d.utils.ArrayUtil
test if array has only one particular value
hasOnlyValuesInt(ArrayList) - Method in class mcib3d.utils.ArrayUtil
test if array has only particular values
hasValue(int) - Method in class mcib3d.utils.ArrayUtil
The value is in the array ?
hide() - Method in class mcib3d.image3d.ImageHandler
 
histogramDistancesBorder(double) - Method in class mcib3d.geom.Objects3DPopulation
Histogram of all distances border to border
histogramDistancesCenter(double) - Method in class mcib3d.geom.Objects3DPopulation
Histogram of all distances center to center
HistogramUtil - Class in mcib3d.utils
/** Copyright (C) 2008- 2011 Thomas Boudier This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
HistogramUtil(double[]) - Constructor for class mcib3d.utils.HistogramUtil
 
hitOrMiss(int, int, Image3D) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
homogenizeBitDepth(ImageHandler[]) - Static method in class mcib3d.image3d.ImageHandler
 
HungarianAlgorithm - Class in mcib3d.tracking_dev
An implementation of the HungarianAlgorithm algorithm for solving the assignment problem.
HungarianAlgorithm(double[][]) - Constructor for class mcib3d.tracking_dev.HungarianAlgorithm
Construct an instance of the algorithm.
hypot(double, double) - Static method in class mcib3d.Jama.util.Maths
sqrt(a^2 + b^2) without under/overflow.
hysteresis(ImagePlus, double, double, boolean, boolean) - Method in class mcib_plugins.Hysteresis_Thresholding
 
hysteresis(Image, double, double) - Method in class mcib_plugins.processing.Thresholder
Applies hysteresis thresholding to an image.
Hysteresis_Thresholding - Class in mcib_plugins
 
Hysteresis_Thresholding() - Constructor for class mcib_plugins.Hysteresis_Thresholding
 
hysteresisLowConnectivity(Image, double, double) - Method in class mcib_plugins.processing.Thresholder
 

I

id - Variable in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
identity(int, int) - Static method in class mcib3d.Jama.Matrix
Generate identity matrix
IJLog - Class in mcib3d.utils.Logger
Created by thomasb on 15/11/16.
IJLog() - Constructor for class mcib3d.utils.Logger.IJLog
 
IJstack - Variable in class mcib3d.image3d.legacy.Image3D
Deprecated.
The ImageJ IJstack that stores the pixels data ( a 1D array could be more efficient )
IJStatus - Class in mcib3d.utils.Logger
Created by thomasb on 15/11/16.
IJStatus() - Constructor for class mcib3d.utils.Logger.IJStatus
 
Image3D - Class in mcib3d.image3d.legacy
Deprecated.
Image3D(int, int, int, int) - Constructor for class mcib3d.image3d.legacy.Image3D
Deprecated.
Constructor for the Image3D object
Image3D(ImageStack) - Constructor for class mcib3d.image3d.legacy.Image3D
Deprecated.
Constructor for the Image3D object from a ImageJ IJstack
ImageByte - Class in mcib3d.image3d
Copyright (C) 2012 Jean Ollion
ImageByte(ImagePlus) - Constructor for class mcib3d.image3d.ImageByte
 
ImageByte(ImageStack) - Constructor for class mcib3d.image3d.ImageByte
 
ImageByte(byte[][], String, int) - Constructor for class mcib3d.image3d.ImageByte
 
ImageByte(String, int, int, int) - Constructor for class mcib3d.image3d.ImageByte
 
ImageByte(int, int, int) - Constructor for class mcib3d.image3d.ImageByte
 
ImageByte(ImageHandler, boolean) - Constructor for class mcib3d.image3d.ImageByte
 
ImageColocalizer - Class in mcib3d.image3d.processing
 
ImageColocalizer(ImagePlus, ImagePlus, Calibration, boolean) - Constructor for class mcib3d.image3d.processing.ImageColocalizer
Creates a new instance of ImageColocalizer
ImageColocalizer(ImagePlus, ImagePlus, boolean) - Constructor for class mcib3d.image3d.processing.ImageColocalizer
Creates a new instance of ImageColocalizer
ImageFloat - Class in mcib3d.image3d
* /** Copyright (C) 2012 Jean Ollion
ImageFloat(ImagePlus) - Constructor for class mcib3d.image3d.ImageFloat
 
ImageFloat(ImageStack) - Constructor for class mcib3d.image3d.ImageFloat
 
ImageFloat(float[][], String, int) - Constructor for class mcib3d.image3d.ImageFloat
 
ImageFloat(String, int, int, int) - Constructor for class mcib3d.image3d.ImageFloat
 
ImageHandler - Class in mcib3d.image3d
Copyright (C) 2012 Jean Ollion
ImageHandler(ImagePlus) - Constructor for class mcib3d.image3d.ImageHandler
 
ImageHandler(ImageStack) - Constructor for class mcib3d.image3d.ImageHandler
 
ImageHandler(String, int, int, int) - Constructor for class mcib3d.image3d.ImageHandler
 
ImageHandler(String, int, int, int, int, int, int) - Constructor for class mcib3d.image3d.ImageHandler
 
ImageInt - Class in mcib3d.image3d
* /** Copyright (C) 2012 Jean Ollion
ImageInt(ImagePlus) - Constructor for class mcib3d.image3d.ImageInt
 
ImageInt(ImageStack) - Constructor for class mcib3d.image3d.ImageInt
 
ImageInt(String, int, int, int) - Constructor for class mcib3d.image3d.ImageInt
 
ImageInt(ImageHandler, boolean) - Constructor for class mcib3d.image3d.ImageInt
 
ImageInt(String, int, int, int, int, int, int) - Constructor for class mcib3d.image3d.ImageInt
 
ImageLabeller - Class in mcib3d.image3d
* /** Copyright (C) 2012 Jean Ollion
ImageLabeller(boolean) - Constructor for class mcib3d.image3d.ImageLabeller
 
ImageLabeller() - Constructor for class mcib3d.image3d.ImageLabeller
 
ImageLabeller(int, int) - Constructor for class mcib3d.image3d.ImageLabeller
 
ImageLabeller.Spot3D - Class in mcib3d.image3d
 
ImageLabeller.Vox3D - Class in mcib3d.image3d
 
ImageLabeller2D - Class in mcib3d.image3d
* /** Copyright (C) 2012 Jean Ollion
ImageLabeller2D(boolean) - Constructor for class mcib3d.image3d.ImageLabeller2D
 
ImageLabeller2D() - Constructor for class mcib3d.image3d.ImageLabeller2D
 
ImageLabeller2D(int, int) - Constructor for class mcib3d.image3d.ImageLabeller2D
 
ImageLabeller2D.Spot2D - Class in mcib3d.image3d
 
ImageLabeller2D.Vox2D - Class in mcib3d.image3d
 
imagePeaks - Variable in class mcib3d.image3d.processing.MaximaFinder
The image with the final peaks
ImagePlus_Utils - Class in mcib3d.image3d
Created by thomasb on 3/3/17.
ImagePlus_Utils() - Constructor for class mcib3d.image3d.ImagePlus_Utils
 
ImageShort - Class in mcib3d.image3d
* /** Copyright (C) 2012 Jean Ollion
ImageShort(ImagePlus) - Constructor for class mcib3d.image3d.ImageShort
Constructor from ImagePlus
ImageShort(ImageStack) - Constructor for class mcib3d.image3d.ImageShort
Constructor from ImageStack
ImageShort(short[][], String, int) - Constructor for class mcib3d.image3d.ImageShort
Generic constructor with array of pixels
ImageShort(String, int, int, int) - Constructor for class mcib3d.image3d.ImageShort
Generic consructor to generate a black image
ImageShort(ImageHandler, boolean) - Constructor for class mcib3d.image3d.ImageShort
Constructor from another generic ImageHandler will convert to write format if necessary
ImageStats - Class in mcib3d.image3d
/** Copyright (C) 2012 Jean Ollion This file is part of tango tango is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
ImageStats(ImageHandler, ImageInt) - Constructor for class mcib3d.image3d.ImageStats
 
img - Variable in class mcib3d.image3d.ImageHandler
 
img - Variable in class mcib3d.image3d.processing.MaximaFinder
The raw image to analyze
Imod - Class in mcib3d.ext
Interface pour imod
Imod() - Constructor for class mcib3d.ext.Imod
Constructor for the Imod object
ImodConf - Class in mcib3d.ext
Parametres de configuration pour Imod
ImodConf() - Constructor for class mcib3d.ext.ImodConf
Constructor for the ImodConf object
ImodConf(String, float, float, float, int, String, boolean) - Constructor for class mcib3d.ext.ImodConf
Constructor for the ImodConf object
inBBox(ArrayList<Point3f>, Point3f) - Method in class mcib3d.geom.deformation3d.Mesh
 
includedInZonesNone(ImageInt) - Method in class mcib3d.geom.Object3D
 
includedInZonesOneMore(ImageInt) - Method in class mcib3d.geom.Object3D
 
includedInZonesOneOnly(ImageInt) - Method in class mcib3d.geom.Object3D
 
includes(Object3D) - Method in class mcib3d.geom.Object3D
 
includesBox(Object3D) - Method in class mcib3d.geom.Object3D
Test if the bouding boxes intersect
includesMarkersNone(ImageInt) - Method in class mcib3d.geom.Object3D
 
includesMarkersOneMore(ImageInt) - Method in class mcib3d.geom.Object3D
 
includesMarkersOneOnly(ImageInt) - Method in class mcib3d.geom.Object3D
 
incrementPairVolume(int, int) - Method in class mcib3d.geom.interactions.InteractionsList
 
incrementPairVolume(int, int, int) - Method in class mcib3d.geom.interactions.InteractionsList
 
incrementVolumeColoc() - Method in class mcib3d.geom.PairColocalisation
 
incrementVolumeColoc(int) - Method in class mcib3d.geom.PairColocalisation
 
indexOf(double) - Method in class mcib3d.utils.ArrayUtil
 
indexOfSumPercent(double) - Method in class mcib3d.utils.ArrayUtil
Index to get x % of the values
init() - Method in class mcib3d.geom.Object3D
Init default values and compute contours and center
init() - Method in class mcib3d.spatial.descriptors.F_Function
 
init() - Method in class mcib3d.spatial.descriptors.G_Border
 
init() - Method in class mcib3d.spatial.descriptors.G_Function
 
init() - Method in class mcib3d.spatial.descriptors.H_Border
 
init() - Method in class mcib3d.spatial.descriptors.H_Function
 
init() - Method in class mcib3d.spatial.descriptors.K_Function
 
init() - Method in interface mcib3d.spatial.descriptors.SpatialDescriptor
 
init() - Method in interface mcib3d.spatial.sampler.SpatialModel
 
init() - Method in class mcib3d.spatial.sampler.SpatialRandom
 
init() - Method in class mcib3d.spatial.sampler.SpatialRandomHardCore
 
init() - Method in class mcib3d.spatial.sampler.SpatialShuffle
 
initial_value - Variable in class mcib_plugins.Filter3D.Filter3Ddefault
 
initializePhase(int) - Method in class mcib3d.tracking_dev.HungarianAlgorithm
Initialize the next phase of the algorithm by clearing the committed workers and jobs sets and by initializing the slack arrays to the values corresponding to the specified root worker.
insert(ImageHandler, int, int, int, boolean) - Method in class mcib3d.image3d.ImageHandler
Insert a 3D image to a specified location
insert(Image3D, int, int, int, boolean) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Insert a 3D image to a specified location
insert2(ImageProcessor, int, boolean) - Method in class mcib3d.align.Align2D
Description of the Method
insertValues(int, ArrayUtil) - Method in class mcib3d.utils.ArrayUtil
 
inside(Point3D) - Method in class mcib3d.geom.Object3D
 
inside(double, double, double) - Method in class mcib3d.geom.Object3D
test if the point is inside the object
insideAll(ArrayList<Point3D>) - Method in class mcib3d.geom.Object3D
 
insideBounding(double, double, double) - Method in class mcib3d.geom.Object3D
test if the point is inside the bounding box of the object
insideBounding(float, float, float) - Method in class mcib3d.geom.Object3D
test if the point is inside the bounding box of the object
insideBounding(double, double, double, int, int, int) - Method in class mcib3d.geom.Object3D
 
insideOne(ArrayList<Point3D>) - Method in class mcib3d.geom.Object3D
 
installComplete() - Static method in class mcib3d.utils.CheckInstall
 
IntCoord3D - Class in mcib3d.geom
 
IntCoord3D() - Constructor for class mcib3d.geom.IntCoord3D
 
IntCoord3D(int, int, int) - Constructor for class mcib3d.geom.IntCoord3D
 
integratedDensity - Variable in class mcib3d.geom.Object3D
Integrated density (sum of pixels)
Interactions - Class in mcib3d.geom.interactions
 
Interactions() - Constructor for class mcib3d.geom.interactions.Interactions
 
Interactions_ - Class in mcib_plugins
 
Interactions_() - Constructor for class mcib_plugins.Interactions_
 
InteractionsCompute - Interface in mcib3d.geom.interactions
 
InteractionsComputeContours - Class in mcib3d.geom.interactions
 
InteractionsComputeContours() - Constructor for class mcib3d.geom.interactions.InteractionsComputeContours
 
InteractionsComputeDamLines - Class in mcib3d.geom.interactions
 
InteractionsComputeDamLines() - Constructor for class mcib3d.geom.interactions.InteractionsComputeDamLines
 
InteractionsComputeDilate - Class in mcib3d.geom.interactions
 
InteractionsComputeDilate(float, float, float) - Constructor for class mcib3d.geom.interactions.InteractionsComputeDilate
 
InteractionsComputeVoronoi - Class in mcib3d.geom.interactions
 
InteractionsComputeVoronoi() - Constructor for class mcib3d.geom.interactions.InteractionsComputeVoronoi
 
InteractionsList - Class in mcib3d.geom.interactions
 
InteractionsList() - Constructor for class mcib3d.geom.interactions.InteractionsList
 
intersection_unit_cube(double, double, double, double, double, double) - Method in class mcib3d.geom.Vector3D
Distance traversée dans un cube (for projection computation)
intersectMask(ImageInt) - Method in class mcib3d.image3d.ImageByte
Deprecated.
intersectMask(ImageHandler) - Method in class mcib3d.image3d.ImageByte
 
intersectMask(ImageInt) - Method in class mcib3d.image3d.ImageFloat
Deprecated.
intersectMask(ImageHandler) - Method in class mcib3d.image3d.ImageFloat
 
intersectMask(ImageFloat) - Method in class mcib3d.image3d.ImageFloat
Deprecated.
intersectMask(ImageInt) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
intersectMask(ImageHandler) - Method in class mcib3d.image3d.ImageHandler
 
intersectMask(ImageInt) - Method in class mcib3d.image3d.ImageShort
Deprecated.
intersectMask(ImageHandler) - Method in class mcib3d.image3d.ImageShort
 
intersectMask2D(ImageInt, int) - Method in class mcib3d.image3d.ImageByte
 
intersectMask2D(ImageInt, int) - Method in class mcib3d.image3d.ImageFloat
 
intersectMask2D(ImageInt, int) - Method in class mcib3d.image3d.ImageHandler
 
intersectMask2D(ImageInt, int) - Method in class mcib3d.image3d.ImageShort
 
intersectTriangle(int, Point3f, Point3f) - Method in class mcib3d.geom.deformation3d.Mesh
 
IntImage3D - Class in mcib3d.image3d.legacy
Deprecated.
IntImage3D(int, int, int) - Constructor for class mcib3d.image3d.legacy.IntImage3D
Deprecated.
constructor (black image)
IntImage3D(int, int, int, int) - Constructor for class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Constructor for the IntImage3D object
IntImage3D(ImageStack) - Constructor for class mcib3d.image3d.legacy.IntImage3D
Deprecated.
constructor from a ImageStack
IntImage3D(ImagePlus) - Constructor for class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
inverse() - Method in class mcib3d.Jama.Matrix
Matrix inverse or pseudoinverse
invert() - Method in class mcib3d.geom.GeomTransform3D
Description of the Method
invert(ImageInt) - Method in class mcib3d.image3d.ImageByte
 
invert(ImageInt) - Method in class mcib3d.image3d.ImageFloat
 
invert(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
invert() - Method in class mcib3d.image3d.ImageHandler
 
invert(ImageInt) - Method in class mcib3d.image3d.ImageShort
 
INVERT - Static variable in class mcib3d.image3d.processing.FastOperation3D
 
invert4x4(double[][], double[][]) - Static method in class mcib3d.geom.GeomTransform3D
taken from volumeJ Invert 4x4 matrix m into inverse mi.
invertBackground(float, float) - Method in class mcib3d.image3d.ImageHandler
 
invertMask(ImageInt) - Method in class mcib3d.image3d.ImageInt
 
invertNormals(ArrayList<Point3f>) - Method in class mcib3d.geom.deformation3d.Mesh
 
invertNormals(List<Point3f>) - Static method in class mcib3d.geom.Object3DSurface
 
IO - Class in mcib3d.geom.deformation3d
 
IO() - Constructor for class mcib3d.geom.deformation3d.IO
 
isBinary(int) - Method in class mcib3d.image3d.ImageInt
 
isBinary() - Method in class mcib3d.image3d.ImageInt
 
isBinary(int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
isCellEditable(int, int) - Method in class mcib_plugins.tools.ResultsTableModel
 
isConcat() - Method in class mcib3d.utils.Logger.TextLog
 
isConnex() - Method in class mcib3d.geom.Object3DVoxels
 
isContour(Voxel3D) - Method in class mcib3d.geom.Object3D
 
isEmpty() - Method in class mcib3d.geom.Object3D
 
isEmpty() - Method in class mcib3d.utils.ArrayUtil
 
isEnd() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
isEqual(ArrayUtil) - Method in class mcib3d.utils.ArrayUtil
test if two arrays are identical
isEqual(ArrayUtil, int, int) - Method in class mcib3d.utils.ArrayUtil
test if two arrays are identical between two indexes
isFullRank() - Method in class mcib3d.Jama.QRDecomposition
Is the matrix full rank?
isIdentity() - Method in class mcib3d.geom.GeomTransform3D
Gets the identity attribute of the GeomTransform3D object
isIn() - Method in class mcib3d.image3d.Coordinate3D
 
isIn(int, int, int) - Method in class mcib3d.image3d.Coordinate3D
 
isIn(int, int, int) - Method in class mcib3d.image3d.MaskIterator
Deprecated.
 
isInsideBoundingBox(int[]) - Method in class mcib3d.geom.Point3D
 
isInsideBoundingBox(int[]) - Method in class mcib3d.geom.Point3DInt
 
isLocalMaximum(int, int, int, float, float, float) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
dit si le pixel donne est un maximum local avec un voisinage donne
isLocalMaximum(int, int, int, float, float, float) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
dit si le pixel donne est un maximum local avec un voisinage donne
isMarked() - Method in class mcib3d.geom.deformation3d.Vertex
 
isMaximum(double) - Method in class mcib3d.utils.ArrayUtil
 
isNew() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
isNonsingular() - Method in class mcib3d.Jama.LUDecomposition
Is the matrix nonsingular?
IsoData() - Method in class mcib3d.utils.ArrayUtil
isodata algorithm (for histogram)
isOpened() - Method in class mcib3d.image3d.ImageByte
 
isOpened() - Method in class mcib3d.image3d.ImageFloat
 
isOpened() - Method in class mcib3d.image3d.ImageHandler
 
isOpened() - Method in class mcib3d.image3d.ImageShort
 
isRoot() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
isSorted() - Method in class mcib3d.utils.ArrayUtil
 
isSPD() - Method in class mcib3d.Jama.CholeskyDecomposition
Is the matrix symmetric and positive definite?
isUpdate() - Method in class mcib3d.utils.Logger.IJLog
 
isValid() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
isValid() - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
isVisible() - Method in class mcib3d.image3d.ImageHandler
 
itemStateChanged(ItemEvent) - Method in class mcib_plugins.ConnectionThresholding_
Description of the Method
itemStateChanged(ItemEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
iterate_and_add(int, int, int, byte) - Method in class mcib_plugins.Filter3D.Filter3Ddefault
 
iterate_and_read(int[]) - Method in class mcib_plugins.Filter3D.Filter3Ddefault
 
iterate_and_subtract(int, int, int, byte) - Method in class mcib_plugins.Filter3D.Filter3Ddefault
 
iterateGlobalScaling(double, int) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
iterateOrientedScaling(Vector3D, double, int) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
iterateRotation(Vector3D, double, double) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
iterateRoughDisplacement(double, int) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
iterateTranslation(double, int) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 

J

jButtonClose - Variable in class mcib3d.image3d.processing.ManualSpot
 
jButtonOK - Variable in class mcib3d.image3d.processing.ManualSpot
 
jPanel - Variable in class mcib_plugins.tools.RoiManager3D_2
 

K

K_Function - Class in mcib3d.spatial.descriptors
 
K_Function(double, double, Object3D) - Constructor for class mcib3d.spatial.descriptors.K_Function
 
kClosestBorder(int) - Method in class mcib3d.geom.ObjectsPopulationDistances
 
kClosestCenter(Object3D, int, boolean) - Method in class mcib3d.geom.Objects3DPopulation
 
kClosestCenter(Object3D, int, ArrayList<Object3D>) - Method in class mcib3d.geom.Objects3DPopulation
 
kClosestCentres(double, double, double, int) - Method in class mcib3d.geom.Objects3DPopulation
 
kClosestDistancesSquared(double, double, double, int) - Method in class mcib3d.geom.Objects3DPopulation
 
kdtree - Variable in class mcib3d.geom.Objects3DPopulation
 
KDTreeC - Class in mcib3d.utils
This is a KD Bucket Tree, for fast sorting and searching of K dimensional data.
KDTreeC(int) - Constructor for class mcib3d.utils.KDTreeC
Constructor with value for dimensions.
KDTreeC(int, int) - Constructor for class mcib3d.utils.KDTreeC
Constructor with value for dimensions and bucket size.
KDTreeC.Item - Class in mcib3d.utils
Item, for moving data around.
kdtreeContours - Variable in class mcib3d.geom.Object3D
kd-tree for the contour
Kernel3D - Class in mcib_plugins.Filter3D
Kernel class to define: - a filter kernel (e.g.
Kernel3D(int) - Constructor for class mcib_plugins.Filter3D.Kernel3D
 
kill() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Kill the Image3D
kMeans_Histogram1D(int[], int, int) - Static method in class mcib3d.utils.ArrayUtil
COPIED FROM ICY (A.

L

labelImage - Variable in class mcib3d.geom.Object3D
label image, starts at 0,0,0
LEFT - Static variable in class mcib_plugins.Filter3D.Kernel3D
 
limit - Variable in class mcib3d.image3d.MaskIterator
Deprecated.
 
line - Variable in class mcib3d.geom.deformation3d.Deriche
 
Line3D_ - Class in mcib_plugins
Description of the Class
Line3D_() - Constructor for class mcib_plugins.Line3D_
 
linreg(int[], int[], int, int) - Method in class mcib3d.image3d.processing.ImageColocalizer
 
linregCostes(int[], int[], int, int) - Method in class mcib3d.image3d.processing.ImageColocalizer
 
LireMessages(String) - Method in class mcib3d.utils.Message
Description of the Method
LireMessages(BufferedReader) - Method in class mcib3d.utils.Message
Description of the Method
LireMessages(BufferedReader, String) - Method in class mcib3d.utils.Message
Description of the Method
LireMessages(String, String) - Method in class mcib3d.utils.Message
Description of the Method
LireMessagesFromJar(String, String, String) - Method in class mcib3d.utils.Message
Description of the Method
list - Variable in class mcib_plugins.tools.RoiManager3D_2
 
listSpots - Variable in class mcib3d.image3d.ImageLabeller
 
listSpots - Variable in class mcib3d.image3d.ImageLabeller2D
 
listValues(ImageHandler) - Method in class mcib3d.geom.Object3D
Outputs the list of Voxels values using intensity image
listValues(ImageHandler, float) - Method in class mcib3d.geom.Object3D
Outputs the list of Voxels values using intensity image above a fixed threshold
listValues(ImageHandler) - Method in class mcib3d.geom.Object3DLabel
 
listValues(ImageHandler, float) - Method in class mcib3d.geom.Object3DLabel
 
listValues(ImageHandler) - Method in class mcib3d.geom.Object3DSurface
 
listValues(ImageHandler, float) - Method in class mcib3d.geom.Object3DSurface
 
listValues(ImageHandler) - Method in class mcib3d.geom.Object3DVoxels
 
listValues(ImageHandler, float) - Method in class mcib3d.geom.Object3DVoxels
 
listVoxels(ImageHandler) - Method in class mcib3d.geom.Object3D
gets the list of all pixels within an image as an ArrayList
listVoxels(ImageHandler, double) - Method in class mcib3d.geom.Object3D
List Voxels in the image with values > threshold
listVoxels(ImageHandler, double, double) - Method in class mcib3d.geom.Object3D
List Voxels in the image with values > threshold0 and < threshold1
listVoxels(ImageHandler) - Method in class mcib3d.geom.Object3DFuzzy
 
listVoxels(ImageHandler, double) - Method in class mcib3d.geom.Object3DLabel
 
listVoxels(ImageHandler, double, double) - Method in class mcib3d.geom.Object3DLabel
 
listVoxels(ImageHandler, double) - Method in class mcib3d.geom.Object3DSurface
 
listVoxels(ImageHandler, double, double) - Method in class mcib3d.geom.Object3DSurface
 
listVoxels(ImageHandler, double) - Method in class mcib3d.geom.Object3DVoxels
 
listVoxels(ImageHandler, double, double) - Method in class mcib3d.geom.Object3DVoxels
 
listVoxels(ImageHandler, int, int, int) - Method in class mcib3d.geom.Object3DVoxels
 
listVoxels(List<Object3D>, ImageHandler) - Static method in class mcib_plugins.tools.Manager3DMeasurements
 
listVoxelsByDistance(Point3D, double, double, boolean) - Method in class mcib3d.geom.Object3D
List Voxels in the image with with distances in specific range from a reference point
loadDataARFF(String) - Method in class mcib3d.Classification.DataSet
 
loadInfo(BufferedReader) - Method in class mcib3d.geom.Object3D
 
loadObject(String, String) - Method in class mcib3d.geom.Object3DVoxels
 
loadObjects(String) - Method in class mcib3d.geom.Objects3DPopulation
 
LOCAL_CONSTANT - Static variable in class mcib3d.image3d.Segment3DSpots
 
LOCAL_DIFF - Static variable in class mcib3d.image3d.Segment3DSpots
 
LOCAL_GAUSS - Static variable in class mcib3d.image3d.Segment3DSpots
 
LOCAL_MEAN - Static variable in class mcib3d.image3d.Segment3DSpots
 
localMean(int, int, int) - Method in class mcib3d.image3d.Segment3DSpots
Local mean for segmentation
localMean(int) - Method in class mcib3d.utils.ArrayUtil
local mean filtering
localMinMax(float[], int, boolean) - Method in class mcib3d.geom.deformation3d.Deriche
 
localThickness(ImageHandler, ImageInt, float, float, float, boolean, int) - Static method in class mcib3d.image3d.distanceMap3d.EDT
Deprecated.
localThickness(ImageHandler, ImageInt, float, boolean, int) - Static method in class mcib3d.image3d.distanceMap3d.EDT
Deprecated.
LocalThickness - Class in mcib3d.image3d.distanceMap3d
Deprecated.
LocalThickness() - Constructor for class mcib3d.image3d.distanceMap3d.LocalThickness
Deprecated.
 
log(String) - Method in class mcib3d.utils.Logger.AbstractLog
 
log(String) - Method in class mcib3d.utils.Logger.IJLog
 
log(String) - Method in class mcib3d.utils.Logger.IJStatus
 
log(String) - Method in class mcib3d.utils.Logger.NoLog
 
log(String) - Method in class mcib3d.utils.Logger.TextLog
 
LoG3D - Class in mcib_plugins.processing
 
LoG3D(boolean) - Constructor for class mcib_plugins.processing.LoG3D
 
logMath() - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Compute the log of the image
lu() - Method in class mcib3d.Jama.Matrix
LU Decomposition
LUDecomposition - Class in mcib3d.Jama
LU Decomposition.
LUDecomposition(Matrix) - Constructor for class mcib3d.Jama.LUDecomposition
LU Decomposition

M

main(String[]) - Static method in class mcib3d.image3d.processing.ManualSpot
 
main(String[]) - Static method in class mcib3d.Jama.test.TestMatrix
Description of the Method
main(String[]) - Static method in class mcib_plugins.tools.RoiManager3D_2
 
Manager3DMeasurements - Class in mcib_plugins.tools
 
Manager3DMeasurements() - Constructor for class mcib_plugins.tools.Manager3DMeasurements
 
Manual_Spot - Class in mcib_plugins.segmentation
 
Manual_Spot() - Constructor for class mcib_plugins.segmentation.Manual_Spot
 
ManualSpot - Class in mcib3d.image3d.processing
 
ManualSpot() - Constructor for class mcib3d.image3d.processing.ManualSpot
Creates new form ManualSpot
ManualSpot(ImagePlus, ImagePlus, int) - Constructor for class mcib3d.image3d.processing.ManualSpot
 
ManualSpot(ImagePlus, ImagePlus) - Constructor for class mcib3d.image3d.processing.ManualSpot
 
maskContains(int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
MaskIterator - Class in mcib3d.image3d
Deprecated.
MaskIterator(ImageHandler) - Constructor for class mcib3d.image3d.MaskIterator
Deprecated.
 
MaskIterator(ImageHandler, float) - Constructor for class mcib3d.image3d.MaskIterator
Deprecated.
 
MaskIterator(int, int, int) - Constructor for class mcib3d.image3d.MaskIterator
Deprecated.
 
match(int, int) - Method in class mcib3d.tracking_dev.HungarianAlgorithm
Helper method to record a matching between worker w and job j.
mathFloatImage(ImageFloat, ImageFloat, int, float, float, int, boolean, AbstractLog) - Static method in class mcib3d.image3d.processing.FastArithmetic3D
 
mathGeneric(ImageFloat, ImageFloat, int, int, int, float, float, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageFloat
Generic arithmetic between images pixel1*parameter1 OPERATION pixel2*parameter2
mathGeneric(ImageInt, ImageInt, int, int, int, float, float, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageInt
Generic arithmetic between images pixel1*parameter1 OPERATION pixel2*parameter2
mathImage(ImageHandler, ImageHandler, int, float, float, int, boolean, AbstractLog) - Static method in class mcib3d.image3d.processing.FastArithmetic3D
 
mathIntImage(ImageInt, ImageInt, int, float, float, int, boolean, AbstractLog) - Static method in class mcib3d.image3d.processing.FastArithmetic3D
 
Maths - Class in mcib3d.Jama.util
Description of the Class
Maths() - Constructor for class mcib3d.Jama.util.Maths
 
Matrix - Class in mcib3d.Jama
ij3d.Jama = Java Matrix class.
Matrix(int, int) - Constructor for class mcib3d.Jama.Matrix
Construct an m-by-n matrix of zeros.
Matrix(int, int, double) - Constructor for class mcib3d.Jama.Matrix
Construct an m-by-n constant matrix.
Matrix(double[][]) - Constructor for class mcib3d.Jama.Matrix
Construct a matrix from a 2-D array.
Matrix(double[][], int, int) - Constructor for class mcib3d.Jama.Matrix
Construct a matrix quickly without checking arguments.
Matrix(double[], int) - Constructor for class mcib3d.Jama.Matrix
Construct a matrix from a one-dimensional packed array
max(IntImage3D) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
MAX - Static variable in class mcib3d.image3d.processing.FastArithmetic3D
 
MAX - Static variable in class mcib3d.image3d.processing.FastFilters3D
 
maxima - Variable in class mcib3d.image3d.processing.MaximaFinder
The list of peaks
MaximaFinder - Class in mcib3d.image3d.processing
 
MaximaFinder(ImageHandler, float) - Constructor for class mcib3d.image3d.processing.MaximaFinder
Constructor with default values for radii
MaximaFinder(ImageHandler, float, float, float) - Constructor for class mcib3d.image3d.processing.MaximaFinder
Constructor
MaximaFinder(ImageHandler) - Constructor for class mcib3d.image3d.processing.MaximaFinder
Constructor with default values
MaximaFinder3D_ - Class in mcib_plugins
 
MaximaFinder3D_() - Constructor for class mcib_plugins.MaximaFinder3D_
 
maximumFilter(float, float, float) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
3D maximum filter
maximumFilter(int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
filtre le volume grace a un filtre maximum 3D
MAXLOCAL - Static variable in class mcib3d.image3d.processing.FastFilters3D
 
maxPixel - Variable in class mcib3d.image3d.legacy.Image3D
Deprecated.
where is the maxPixel pixel
mcib3d.align - package mcib3d.align
 
mcib3d.Classification - package mcib3d.Classification
 
mcib3d.ext - package mcib3d.ext
 
mcib3d.geom - package mcib3d.geom
 
mcib3d.geom.deformation3d - package mcib3d.geom.deformation3d
 
mcib3d.geom.interactions - package mcib3d.geom.interactions
 
mcib3d.image3d - package mcib3d.image3d
 
mcib3d.image3d.comparator - package mcib3d.image3d.comparator
 
mcib3d.image3d.distanceMap3d - package mcib3d.image3d.distanceMap3d
 
mcib3d.image3d.IterativeThresholding - package mcib3d.image3d.IterativeThresholding
 
mcib3d.image3d.legacy - package mcib3d.image3d.legacy
 
mcib3d.image3d.processing - package mcib3d.image3d.processing
 
mcib3d.image3d.regionGrowing - package mcib3d.image3d.regionGrowing
 
mcib3d.Jama - package mcib3d.Jama
 
mcib3d.Jama.test - package mcib3d.Jama.test
 
mcib3d.Jama.util - package mcib3d.Jama.util
 
mcib3d.spatial.analysis - package mcib3d.spatial.analysis
 
mcib3d.spatial.descriptors - package mcib3d.spatial.descriptors
 
mcib3d.spatial.sampler - package mcib3d.spatial.sampler
 
mcib3d.tracking_dev - package mcib3d.tracking_dev
 
mcib3d.utils - package mcib3d.utils
 
mcib3d.utils.Logger - package mcib3d.utils.Logger
 
mcib_plugins - package mcib_plugins
 
mcib_plugins.analysis - package mcib_plugins.analysis
 
mcib_plugins.Filter3D - package mcib_plugins.Filter3D
 
mcib_plugins.processing - package mcib_plugins.processing
 
mcib_plugins.segmentation - package mcib_plugins.segmentation
 
mcib_plugins.tools - package mcib_plugins.tools
 
MEAN - Static variable in class mcib3d.image3d.processing.FastFilters3D
 
meanDensity - Variable in class mcib3d.geom.Object3D
 
meanSquare(ArrayUtil[]) - Method in class mcib3d.align.Align2D
Description of the Method
meanValue - Variable in class mcib3d.image3d.legacy.Image3D
Deprecated.
average value of the image
MEASURE_AREA_PIX - Static variable in class mcib3d.geom.Object3D
 
MEASURE_AREA_UNIT - Static variable in class mcib3d.geom.Object3D
 
MEASURE_COMPACTNESS_UNITS - Static variable in class mcib3d.geom.Object3D
 
MEASURE_COMPACTNESS_VOXELS - Static variable in class mcib3d.geom.Object3D
 
MEASURE_DC_AVG - Static variable in class mcib3d.geom.Object3D
 
MEASURE_DC_SD - Static variable in class mcib3d.geom.Object3D
 
MEASURE_INTENSITY_AVG - Static variable in class mcib3d.geom.Object3D
 
MEASURE_INTENSITY_MAX - Static variable in class mcib3d.geom.Object3D
 
MEASURE_INTENSITY_MEDIAN - Static variable in class mcib3d.geom.Object3D
 
MEASURE_INTENSITY_MIN - Static variable in class mcib3d.geom.Object3D
 
MEASURE_INTENSITY_SD - Static variable in class mcib3d.geom.Object3D
 
MEASURE_MAIN_ELONGATION - Static variable in class mcib3d.geom.Object3D
 
MEASURE_NONE - Static variable in class mcib3d.geom.Object3D
 
MEASURE_VOLUME_PIX - Static variable in class mcib3d.geom.Object3D
 
MEASURE_VOLUME_UNIT - Static variable in class mcib3d.geom.Object3D
 
measurements3D(List<Object3D>) - Static method in class mcib_plugins.tools.Manager3DMeasurements
 
MEDIAN - Static variable in class mcib3d.image3d.processing.FastFilters3D
 
median() - Method in class mcib3d.utils.ArrayUtil
Find median.
medianFilter(int, int, int) - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
filtre le volume grace a un filtre median 3D
medianFilter(float, float, float) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
3D median filter
medianFilter(int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
filtre le volume grace a un filtre median 3D
medianSort() - Method in class mcib3d.utils.ArrayUtil
The median (sorted array)
Mereo_3D - Class in mcib_plugins
/** Copyright (C) 2008- 2012 Thomas Boudier and others This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
Mereo_3D() - Constructor for class mcib_plugins.Mereo_3D
 
MereoAnalysis - Class in mcib3d.geom
 
MereoAnalysis(Objects3DPopulation, Objects3DPopulation) - Constructor for class mcib3d.geom.MereoAnalysis
 
MereoObject3D - Class in mcib3d.geom
* /** Copyright (C) 2008- 2011 Thomas Boudier
MereoObject3D(Object3D, Object3D) - Constructor for class mcib3d.geom.MereoObject3D
 
MereoObject3D(Object3D, Object3D, float, float, float) - Constructor for class mcib3d.geom.MereoObject3D
 
MereoObject3D(Object3D, Object3D, float, float) - Constructor for class mcib3d.geom.MereoObject3D
 
MereoObject3D(Object3D, Object3D, float) - Constructor for class mcib3d.geom.MereoObject3D
 
merge3D(ImageInt[], int, int, int) - Static method in class mcib3d.image3d.ImageHandler
 
merge3DBinary(ImageInt[], int, int, int) - Static method in class mcib3d.image3d.ImageHandler
 
merge3DRaw(ImageHandler[], int, int, int) - Static method in class mcib3d.image3d.ImageHandler
 
mergeLabels(ArrayList<Integer>, ArrayList<Voxel3D>) - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
mergeLabels(int[], ArrayList<Voxel3D>) - Method in class mcib3d.image3d.regionGrowing.RegionGrowing
 
Mesh - Class in mcib3d.geom.deformation3d
 
Mesh(List<Point3f>) - Constructor for class mcib3d.geom.deformation3d.Mesh
 
MeshEditor - Class in mcib3d.geom
/** Copyright (C) 2008- 2011 Thomas Boudier This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
MeshEditor() - Constructor for class mcib3d.geom.MeshEditor
 
Message - Class in mcib3d.utils
classe permettant :
le stockage d'un tableau de float les calculs statistiques sur ce tableau le tri du tableau
Message() - Constructor for class mcib3d.utils.Message
Constructor for the Messages object
messenger - Variable in class mcib_plugins.processing.Thresholder
The object used for message displaying.
methodDILATE - Static variable in class mcib3d.geom.Objects3DPopulationInteractions
 
methodLINE - Static variable in class mcib3d.geom.Objects3DPopulationInteractions
 
methodTOUCH - Static variable in class mcib3d.geom.Objects3DPopulationInteractions
 
min(IntImage3D) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
MIN - Static variable in class mcib3d.image3d.processing.FastArithmetic3D
 
MIN - Static variable in class mcib3d.image3d.processing.FastFilters3D
 
minAndMaxSet() - Method in class mcib3d.image3d.ImageStats
 
miniLabelImage - Variable in class mcib3d.geom.Object3D
The image where the object lies with offset usually xmin, ymin and zmin
minimumFilter(float, float, float) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
3D minimum filter
minimumFilter(int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
filtre le volume grace a un filtre minimum 3D
minMax(float[]) - Method in class mcib3d.geom.deformation3d.Deriche
 
minPixel - Variable in class mcib3d.image3d.legacy.Image3D
Deprecated.
where is the minPixel pixel
minus(Matrix) - Method in class mcib3d.Jama.Matrix
C = A - B
minusEquals(Matrix) - Method in class mcib3d.Jama.Matrix
A = A - B
Mitosis - Class in mcib3d.tracking_dev
 
Mitosis(Object3D, Object3D) - Constructor for class mcib3d.tracking_dev.Mitosis
 
MitosisDetector - Class in mcib3d.tracking_dev
 
MitosisDetector(ImageHandler, ImageHandler, Association) - Constructor for class mcib3d.tracking_dev.MitosisDetector
 
MM(int, int) - Method in class mcib3d.image3d.processing.ImageColocalizer
 
model - Variable in class mcib_plugins.tools.RoiManager3D_2
 
momentsSet() - Method in class mcib3d.image3d.ImageStats
 
MORPHO_CLOSE - Static variable in class mcib3d.image3d.processing.BinaryMorpho
 
MORPHO_DILATE - Static variable in class mcib3d.image3d.processing.BinaryMorpho
 
MORPHO_ERODE - Static variable in class mcib3d.image3d.processing.BinaryMorpho
 
MORPHO_OPEN - Static variable in class mcib3d.image3d.processing.BinaryMorpho
 
mouseClicked(MouseEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
mouseEntered(MouseEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
mouseExited(MouseEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
mousePressed(MouseEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
mouseReleased(MouseEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
mouseWheelMoved(MouseWheelEvent) - Method in class mcib_plugins.tools.RoiManager3D_2
 
MULT - Static variable in class mcib3d.image3d.processing.FastArithmetic3D
 
MULT - Static variable in class mcib3d.image3d.processing.FastOperation3D
 
Multi_Coloc - Class in mcib_plugins
* /** Copyright (C) 2008- 2012 Thomas Boudier and others
Multi_Coloc() - Constructor for class mcib_plugins.Multi_Coloc
 
multiply(double) - Method in class mcib3d.geom.Vector3D
multiply a vector by a scalar
multiply(double, double, double) - Method in class mcib3d.geom.Vector3D
mumultiply the coordinates
multiplyBy(float) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
multiplies all pixels by a given value
multiplyBy(Image3D) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
 
multiplyByValue(float) - Method in class mcib3d.image3d.ImageHandler
 
multiplyImage(ImageHandler, float) - Method in class mcib3d.image3d.ImageHandler
Compute the operation coeff*this*other;
multiplyMe(double) - Method in class mcib3d.geom.Vector3D
multiply current vector by a scalar
multiplyMe(double, double, double) - Method in class mcib3d.geom.Vector3D
mumultiply the coordinates
multiThread - Variable in class mcib3d.geom.Object3D
use multithreading mode (not used ?)
multithread - Variable in class mcib3d.image3d.legacy.Image3D
Deprecated.
 
multithread - Variable in class mcib3d.image3d.Segment3DSpots
 

N

name - Variable in class mcib3d.geom.Object3D
name the object (not used yet)
nbConnexite2D(int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Description of the Method
nbCpus - Variable in class mcib3d.image3d.processing.MaximaFinder
The number of cpus to use, 0 = all
nbdecouleur - Variable in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Description of the Field
nbNeighbor(int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Number of neighborhood pixels
nbVoxContourOverlap(boolean, boolean) - Method in class mcib3d.geom.MereoObject3D
 
newBlankImageFloat(String, ImageHandler) - Static method in class mcib3d.image3d.ImageFloat
 
newBlankImageHandler(String, ImageHandler) - Static method in class mcib3d.image3d.ImageHandler
 
newPosition(Point3f, Point3f, float) - Method in class mcib3d.geom.deformation3d.Deriche
 
newPositionF(Point3f, Point3f, float) - Method in class mcib3d.geom.deformation3d.Deriche
 
Newst2() - Method in class mcib3d.ext.Imod
Description of the Method
Newst2(String) - Method in class mcib3d.ext.Imod
Création d'un fichier newst2.com (correction du bug ,10)
nlLaplacien(int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
3D non linear laplacien
noiseTolerance - Variable in class mcib3d.image3d.processing.MaximaFinder
The noise tolerance around each peak
NoLog - Class in mcib3d.utils.Logger
Created by thomasb on 18/4/17.
NoLog() - Constructor for class mcib3d.utils.Logger.NoLog
 
nonLinearLaplacianFilter(int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
3D non linear laplacian (version 2)
nonLinearLaplacianFilter(int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
filtre le volume grace a un filtre laplacien non lineaire
NonTangentialProperParthood() - Method in class mcib3d.geom.MereoObject3D
 
NonTangentialProperParthoodInverse() - Method in class mcib3d.geom.MereoObject3D
 
norm1() - Method in class mcib3d.Jama.Matrix
One norm
norm2() - Method in class mcib3d.Jama.Matrix
Two norm
norm2() - Method in class mcib3d.Jama.SingularValueDecomposition
Two norm
normaliseLabel(ImageInt, ImageFloat) - Static method in class mcib3d.image3d.distanceMap3d.EDT
 
normaliseValue(float, float) - Method in class mcib3d.image3d.ImageHandler
 
normalization(Point3f) - Method in class mcib3d.geom.deformation3d.Mesh
 
normalize(float[], float) - Method in class mcib3d.geom.deformation3d.Deriche
 
normalize() - Method in class mcib3d.geom.Vector3D
normalization of the vector, put length to 1.0
normalize(double, double) - Method in class mcib3d.image3d.ImageByte
 
normalize(double, double) - Method in class mcib3d.image3d.ImageFloat
 
normalize(double, double) - Method in class mcib3d.image3d.ImageHandler
 
normalize(ImageInt, double) - Method in class mcib3d.image3d.ImageHandler
 
normalize(double, double) - Method in class mcib3d.image3d.ImageShort
 
normalize_(ImageInt, double) - Method in class mcib3d.image3d.BlankMask
 
normalize_(ImageInt, double) - Method in class mcib3d.image3d.ImageByte
 
normalize_(ImageInt, double) - Method in class mcib3d.image3d.ImageFloat
 
normalize_(ImageInt, double) - Method in class mcib3d.image3d.ImageHandler
 
normalize_(ImageInt, double) - Method in class mcib3d.image3d.ImageShort
 
normalizeDistanceMap(ImageFloat, ImageInt) - Static method in class mcib3d.image3d.distanceMap3d.EDT
 
normalizeDistanceMap(ImageFloat, ImageInt, boolean) - Static method in class mcib3d.image3d.distanceMap3d.EDT
 
normalizeDistanceMap(ImageFloat, ImageHandler, boolean) - Static method in class mcib3d.image3d.distanceMap3d.EDT
 
normF() - Method in class mcib3d.Jama.Matrix
Frobenius norm
normInf() - Method in class mcib3d.Jama.Matrix
Infinity norm
NTPP - Static variable in class mcib3d.geom.MereoObject3D
 
NTPPi - Static variable in class mcib3d.geom.MereoObject3D
 
Numbering_ - Class in mcib_plugins
* /** Copyright (C) 2008- 2012 Thomas Boudier and others
Numbering_() - Constructor for class mcib_plugins.Numbering_
 

O

obj - Variable in class mcib3d.utils.KDTreeC.Item
 
Object3D - Class in mcib3d.geom
Copyright (C) 2008- 2011 Thomas Boudier
Object3D() - Constructor for class mcib3d.geom.Object3D
 
Object3D_IJUtils - Class in mcib3d.geom
static methods to use with ImageJ for the Object3D class Created by thomasb on 16/11/16.
Object3D_IJUtils() - Constructor for class mcib3d.geom.Object3D_IJUtils
 
Object3DFactory - Class in mcib3d.geom
Deprecated.
Object3DFactory(ImageInt) - Constructor for class mcib3d.geom.Object3DFactory
Deprecated.
 
Object3DFactory.ObjectValueComparator - Class in mcib3d.geom
Deprecated.
 
Object3DFuzzy - Class in mcib3d.geom
 
Object3DFuzzy(int, LinkedList<Voxel3D>) - Constructor for class mcib3d.geom.Object3DFuzzy
 
Object3DLabel - Class in mcib3d.geom
* /** Copyright (C) 2008- 2011 Thomas Boudier
Object3DLabel(ImageInt, int) - Constructor for class mcib3d.geom.Object3DLabel
constructor
Object3DLabel(ImagePlus, int) - Constructor for class mcib3d.geom.Object3DLabel
Deprecated.
Object3DPoint - Class in mcib3d.geom
 
Object3DPoint(int, Point3D) - Constructor for class mcib3d.geom.Object3DPoint
 
Object3DPoint(int, double, double, double) - Constructor for class mcib3d.geom.Object3DPoint
 
Object3DSurface - Class in mcib3d.geom
* /** Copyright (C) 2008- 2011 Thomas Boudier
Object3DSurface(List<Point3f>) - Constructor for class mcib3d.geom.Object3DSurface
 
Object3DSurface(List<Point3f>, int) - Constructor for class mcib3d.geom.Object3DSurface
 
Object3DVoxels - Class in mcib3d.geom
/** Copyright (C) 2008- 2011 Thomas Boudier
Object3DVoxels() - Constructor for class mcib3d.geom.Object3DVoxels
 
Object3DVoxels(int) - Constructor for class mcib3d.geom.Object3DVoxels
 
Object3DVoxels(ImageHandler, int) - Constructor for class mcib3d.geom.Object3DVoxels
constructor
Object3DVoxels(ImageHandler) - Constructor for class mcib3d.geom.Object3DVoxels
 
Object3DVoxels(ImageHandler, ImageHandler) - Constructor for class mcib3d.geom.Object3DVoxels
 
Object3DVoxels(ImagePlus, int) - Constructor for class mcib3d.geom.Object3DVoxels
Deprecated.
use Object3D-IJUtils Constructor for the Object3D object
Object3DVoxels(ImageStack, int) - Constructor for class mcib3d.geom.Object3DVoxels
Deprecated.
use Object3D-IJUtils Constructor for the Object3D object
Object3DVoxels(LinkedList<Voxel3D>) - Constructor for class mcib3d.geom.Object3DVoxels
 
Object3DVoxels(Object3DVoxels) - Constructor for class mcib3d.geom.Object3DVoxels
copy
Object3DVoxels(Object3D) - Constructor for class mcib3d.geom.Object3DVoxels
 
OBJECT_1 - Static variable in class mcib_plugins.tools.ResultsFrame
 
OBJECT_NO - Static variable in class mcib_plugins.tools.ResultsFrame
 
ObjectCreator3D - Class in mcib3d.geom
Copyright (C) Thomas Boudier
ObjectCreator3D(ImageHandler) - Constructor for class mcib3d.geom.ObjectCreator3D
Constructor for the ObjectCreator3D object
ObjectCreator3D(ImageStack) - Constructor for class mcib3d.geom.ObjectCreator3D
 
ObjectCreator3D(int, int, int) - Constructor for class mcib3d.geom.ObjectCreator3D
Constructor for the ObjectCreator3D object
ObjectCreator_ - Class in mcib_plugins
Description of the Class
ObjectCreator_() - Constructor for class mcib_plugins.ObjectCreator_
 
ObjectDistBB - Class in mcib3d.geom
 
ObjectDistBB(Object3D, double) - Constructor for class mcib3d.geom.ObjectDistBB
 
Objects3DPopulation - Class in mcib3d.geom
 
Objects3DPopulation() - Constructor for class mcib3d.geom.Objects3DPopulation
Conctructor
Objects3DPopulation(Object3D[]) - Constructor for class mcib3d.geom.Objects3DPopulation
 
Objects3DPopulation(ArrayList<Object3D>) - Constructor for class mcib3d.geom.Objects3DPopulation
 
Objects3DPopulation(Object3D[], Calibration) - Constructor for class mcib3d.geom.Objects3DPopulation
Deprecated.
Objects3DPopulation(ImagePlus) - Constructor for class mcib3d.geom.Objects3DPopulation
Deprecated.
Objects3DPopulation(ImageHandler, int) - Constructor for class mcib3d.geom.Objects3DPopulation
 
Objects3DPopulation(ImageInt, int) - Constructor for class mcib3d.geom.Objects3DPopulation
 
objects3DPopulation - Variable in class mcib_plugins.tools.RoiManager3D_2
 
Objects3DPopulationAnalysis - Class in mcib3d.geom
Deprecated.
Objects3DPopulationAnalysis(ImagePlus) - Constructor for class mcib3d.geom.Objects3DPopulationAnalysis
Deprecated.
 
Objects3DPopulationAnalysis() - Constructor for class mcib3d.geom.Objects3DPopulationAnalysis
Deprecated.
 
Objects3DPopulationColocalisation - Class in mcib3d.geom
Public class to compute (fast) co-localisation between two images
Objects3DPopulationColocalisation(Objects3DPopulation, Objects3DPopulation) - Constructor for class mcib3d.geom.Objects3DPopulationColocalisation
Constructor with two populations of objects
Objects3DPopulationInteractions - Class in mcib3d.geom
 
Objects3DPopulationInteractions(ImageHandler) - Constructor for class mcib3d.geom.Objects3DPopulationInteractions
 
Objects3DPopulationInteractions(int, ImageHandler) - Constructor for class mcib3d.geom.Objects3DPopulationInteractions
 
OBJECTS_2 - Static variable in class mcib_plugins.tools.ResultsFrame
 
ObjectsPopulationDistances - Class in mcib3d.geom
 
ObjectsPopulationDistances(Objects3DPopulation) - Constructor for class mcib3d.geom.ObjectsPopulationDistances
 
ObjectTrack - Class in mcib3d.image3d.IterativeThresholding
* /** Copyright (C) 2008- 2012 Thomas Boudier and others
ObjectTrack() - Constructor for class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
ObjectValueComparator() - Constructor for class mcib3d.geom.Object3DFactory.ObjectValueComparator
Deprecated.
 
offsetCostes(int, int, int) - Method in class mcib3d.image3d.processing.ImageColocalizer
 
offsetX - Variable in class mcib3d.image3d.ImageHandler
 
offsetY - Variable in class mcib3d.image3d.ImageHandler
 
offsetZ - Variable in class mcib3d.image3d.ImageHandler
 
open(String) - Method in class mcib3d.utils.StackFolderOpener
Description of the Method
open(String, boolean) - Method in class mcib3d.utils.StackFolderOpener
ouvre les images d'un repertoire sous la forme d'un stack
OPENGRAY - Static variable in class mcib3d.image3d.processing.FastFilters3D
 
openImage(File) - Static method in class mcib3d.image3d.ImageHandler
 
opening3D(int, int, int, int, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Ouverture binaire 3D, normalement les objets sont noir sur fond blanc
opening3D(Image3D, int, boolean) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Ouverture binaire 3D avec kernel, normalement les objets sont noir sur fond blanc
opening3D(int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Ouverture binaire 3D, normalement les objets sont noir sur fond blanc
opening3D(Image3D, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Ouverture binaire 3D avec kernel, normalement les objets sont noir sur fond blanc
operationFloatImage(ImageFloat, int, float, float, int, boolean, AbstractLog) - Static method in class mcib3d.image3d.processing.FastOperation3D
 
operationGeneric(ImageFloat, int, int, int, float, float, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageFloat
 
operationGeneric(ImageInt, int, int, int, float, float, Chrono, AbstractLog) - Method in class mcib3d.image3d.ImageInt
 
operationImage(ImageHandler, int, float, float) - Static method in class mcib3d.image3d.processing.FastOperation3D
 
operationImage(ImageHandler, int, float, float, int, boolean, AbstractLog) - Static method in class mcib3d.image3d.processing.FastOperation3D
 
operationIntImage(ImageInt, int, float, float, int, boolean, AbstractLog) - Static method in class mcib3d.image3d.processing.FastOperation3D
 
opposite() - Method in class mcib3d.image3d.ImageFloat
 
orderedDistancesBorderObjects(Object3D) - Method in class mcib3d.geom.Objects3DPopulationAnalysis
Deprecated.
orderedDistancesCenterObjects(Object3D) - Method in class mcib3d.geom.Objects3DPopulationAnalysis
Deprecated.
 
ouverture3D(int, int, int, int, boolean) - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Ouverture binaire 3D, normalement les objets sont noir sur fond blanc
ouverture3D(int, int, int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
Overlap(int, int) - Method in class mcib3d.image3d.processing.ImageColocalizer
 
overlapBox(Object3D) - Method in class mcib3d.geom.Object3D
 

P

PairColocalisation - Class in mcib3d.geom
 
PairColocalisation(Object3D, Object3D) - Constructor for class mcib3d.geom.PairColocalisation
 
PairColocalisation(Object3D, Object3D, int) - Constructor for class mcib3d.geom.PairColocalisation
 
PartialOverlap() - Method in class mcib3d.geom.MereoObject3D
 
pcColoc(Object3D) - Method in class mcib3d.geom.Object3D
Percentage of colocalisation between two objects relative to this object
pcColoc2(ArrayList<Object3DVoxels>) - Method in class mcib3d.geom.Object3DVoxels
 
pcColocA() - Method in class mcib3d.geom.MereoObject3D
 
pcColocB() - Method in class mcib3d.geom.MereoObject3D
 
pcColocSum(Object3D, Object3D) - Static method in class mcib3d.geom.Object3D
 
pixels - Variable in class mcib3d.image3d.ImageByte
 
pixels - Variable in class mcib3d.image3d.ImageFloat
 
pixels - Variable in class mcib3d.image3d.ImageShort
 
pixmax - Variable in class mcib3d.geom.Object3D
Max pix value in object
pixmin - Variable in class mcib3d.geom.Object3D
Min pix value in object
plotCumulHistogram(String) - Method in class mcib3d.utils.HistogramUtil
 
plotHistogram(String) - Method in class mcib3d.utils.HistogramUtil
 
plus(Matrix) - Method in class mcib3d.Jama.Matrix
C = A + B
plusEquals(Matrix) - Method in class mcib3d.Jama.Matrix
A = A + B
pnt - Variable in class mcib3d.utils.KDTreeC.Item
 
PO - Static variable in class mcib3d.geom.MereoObject3D
 
Point3D - Class in mcib3d.geom
Copyright (C) Thomas Boudier License: This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
Point3D() - Constructor for class mcib3d.geom.Point3D
Constructor for the Point3D object
Point3D(double, double, double) - Constructor for class mcib3d.geom.Point3D
Constructor for the Point3D object
Point3D(Point3D) - Constructor for class mcib3d.geom.Point3D
Constructor for the Point3D object
Point3D(Point3f) - Constructor for class mcib3d.geom.Point3D
 
Point3DInt - Class in mcib3d.geom
 
Point3DInt(int, int, int) - Constructor for class mcib3d.geom.Point3DInt
 
pointPixelBorder(double, double, double, Vector3D) - Method in class mcib3d.geom.Object3D
Vector from a point along a direction to the border of the object
post_process_voxel(double, double) - Method in class mcib_plugins.Filter3D.Filter3Ddefault
 
post_process_voxel(double, double) - Method in class mcib_plugins.Filter3D.Filter3Dmax
 
post_process_voxel(double, double) - Method in class mcib_plugins.Filter3D.Filter3DmaxLocal
 
post_process_voxel(double, double) - Method in class mcib_plugins.Filter3D.Filter3Dmean
 
post_process_voxel(double, double) - Method in class mcib_plugins.Filter3D.Filter3Dmin
 
POW - Static variable in class mcib3d.image3d.processing.FastOperation3D
 
powImage(double) - Method in class mcib3d.image3d.ImageHandler
 
Prenewst() - Method in class mcib3d.ext.Imod
Description of the Method
print() - Method in class mcib3d.image3d.Coordinate3D
 
print(int, int) - Method in class mcib3d.Jama.Matrix
Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class mcib3d.Jama.Matrix
Print the matrix to the output stream.
print(NumberFormat, int) - Method in class mcib3d.Jama.Matrix
Print the matrix to stdout.
print(PrintWriter, NumberFormat, int) - Method in class mcib3d.Jama.Matrix
Print the matrix to the output stream.
print(Throwable, String, boolean) - Static method in class mcib3d.utils.exceptionPrinter
 
process(ImageHandler, int, int, boolean) - Static method in class mcib3d.image3d.processing.FillHoles3D
 
process(ImageByte, int, int, boolean) - Static method in class mcib3d.image3d.processing.FillHoles3D
 
process(ImageShort, int, int, boolean) - Static method in class mcib3d.image3d.processing.FillHoles3D
 
process(ImagePlus, ImagePlus, String, boolean, boolean, boolean) - Method in class mcib_plugins.analysis.spatialAnalysis
 
process1D() - Method in class mcib3d.image3d.distanceMap3d.EDT_1D
 
process_next_voxel(int, int, int, Filter3Ddefault.Voxel_value, byte) - Method in class mcib_plugins.Filter3D.Filter3Ddefault
 
process_next_voxel(int, int, int, Filter3Ddefault.Voxel_value, byte) - Method in class mcib_plugins.Filter3D.Filter3Dmax
 
process_next_voxel(int, int, int, Filter3Ddefault.Voxel_value, byte) - Method in class mcib_plugins.Filter3D.Filter3DmaxLocal
 
process_next_voxel(int, int, int, Filter3Ddefault.Voxel_value, byte) - Method in class mcib_plugins.Filter3D.Filter3Dmean
 
process_next_voxel(int, int, int, Filter3Ddefault.Voxel_value, byte) - Method in class mcib_plugins.Filter3D.Filter3Dmin
 
process_voxel(double, double) - Method in class mcib_plugins.Filter3D.Filter3Ddefault
 
process_voxel(double, double) - Method in class mcib_plugins.Filter3D.Filter3Dmax
 
process_voxel(double, double) - Method in class mcib_plugins.Filter3D.Filter3DmaxLocal
 
process_voxel(double, double) - Method in class mcib_plugins.Filter3D.Filter3Dmean
 
process_voxel(double, double) - Method in class mcib_plugins.Filter3D.Filter3Dmin
 
processAll(ImageHandler, ImageHandler, boolean, boolean, boolean) - Method in class mcib_plugins.analysis.spatialAnalysis
 
processAll(ImagePlus, ImagePlus, boolean, boolean, boolean) - Method in class mcib_plugins.analysis.spatialAnalysis
 
progressor - Variable in class mcib_plugins.processing.Thresholder
The object used for progress displaying.
project(int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
project(Vector3D, Vector3D, boolean) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
projectAVG(String) - Method in class mcib3d.image3d.ImageInt
 
projection(int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Average projection
projection(Vector3D, Vector3D, boolean) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
projectionInterpolated(Vector3D, boolean) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Projection by interpolation
projectionPlane(double, double, double, double) - Method in class mcib3d.geom.Point3D
 
projectionX(int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Description of the Method
projectionY(int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Description of the Method
projectionZ(int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Description of the Method
projectionZ(int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Description of the Method
propagation(IntImage3D, int, int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Propagation of a value to connected pixels
propagation27(int, int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Propagation of a value to connected pixels
propagation2D(int, int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Description of the Method
propagation6(int, int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Propagation of a value to connected pixels
propagationConditionnelle(IntImage3D, int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Description of the Method
ProperParthood() - Method in class mcib3d.geom.MereoObject3D
 
ProperParthoodInverse() - Method in class mcib3d.geom.MereoObject3D
 
PSPC - Static variable in class mcib3d.align.Align3D
Description of the Field
putPixel(int, int, int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
donne une valeur au pixel de coordonnees (x,y,z)
putPixel(int, int, int, double) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
 
putPixel(int, int, int, float) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Sets the pixel value at position (x,y,z)
putPixel(int, int, int, double) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
putValue(int, double) - Method in class mcib3d.utils.ArrayUtil
put a value to a index

Q

qr() - Method in class mcib3d.Jama.Matrix
QR Decomposition
QRDecomposition - Class in mcib3d.Jama
QR Decomposition.
QRDecomposition(Matrix) - Constructor for class mcib3d.Jama.QRDecomposition
QR Decomposition, computed by Householder reflections.
quantif3D(List<Object3D>, ImageHandler) - Static method in class mcib_plugins.tools.Manager3DMeasurements
 

R

RA - Static variable in class mcib3d.align.Align3D
Description of the Field
Radial_3D - Class in mcib_plugins
plugin de filtrage anisotropique 3D
Radial_3D() - Constructor for class mcib_plugins.Radial_3D
 
radialDistribution(int, int, int, int, ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
radialDistribution(int, int, int, int, int, ImageHandler) - Method in class mcib3d.image3d.ImageHandler
Radial distribution of pixels mean values in layers
radialDistribution(int, int, int, int) - Method in class mcib3d.image3d.ImageHandler
Radial distribution of pixels mean values in layers
radialDistribution(int, int, int, int, IntImage3D) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Radial distribution of pixels mean values in layers
radialDistribution(int, int, int, int) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Radial distribution of pixels mean values in layers
radiusCenter(Object3D) - Method in class mcib3d.geom.Object3D
the radius of the object towards another object
radiusCenter(Object3D, boolean) - Method in class mcib3d.geom.Object3D
the radius of the object towards another object, in forward or opposite direction
radiusCenter(Vector3D) - Method in class mcib3d.geom.Object3D
the radius along a direction
radiusPixel(double, double, double) - Method in class mcib3d.geom.Object3D
the radius towards a point
radXY - Variable in class mcib3d.image3d.processing.MaximaFinder
The radius XY to find local maxima
radZ - Variable in class mcib3d.image3d.processing.MaximaFinder
The radius Z to find local maxima
random(int, int) - Static method in class mcib3d.Jama.Matrix
Generate matrix with random elements
rank() - Method in class mcib3d.Jama.Matrix
Matrix rank
rank() - Method in class mcib3d.Jama.SingularValueDecomposition
Effective numerical matrix rank
rank(ArrayUtil, ArrayUtil[], ArrayUtil, ArrayUtil) - Static method in class mcib3d.utils.CDFTools
 
Raw2MRC(String, String, int, int, int, String) - Method in class mcib3d.ext.Imod
Description of the Method
rawImage - Variable in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
RDAR - Class in mcib3d.geom
Created by thomasb on 19/7/16.
RDAR(Object3DVoxels) - Constructor for class mcib3d.geom.RDAR
 
RDAR_ - Class in mcib_plugins
Created by thomasb on 19/7/16.
RDAR_() - Constructor for class mcib_plugins.RDAR_
 
read(BufferedReader) - Static method in class mcib3d.Jama.Matrix
Read a matrix from a stream.
RealImage3D - Class in mcib3d.image3d.legacy
Deprecated.
RealImage3D(int, int, int) - Constructor for class mcib3d.image3d.legacy.RealImage3D
Deprecated.
constructeur d'un volume vide (noir)
RealImage3D(int, int, int, float[][]) - Constructor for class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Constructor for the RealImage3D object
RealImage3D(ImageStack) - Constructor for class mcib3d.image3d.legacy.RealImage3D
Deprecated.
constructeur d'un volume a partir d'un IJstack
RealImage3D(ImagePlus) - Constructor for class mcib3d.image3d.legacy.RealImage3D
Deprecated.
 
RealImage3D(ImageProcessor) - Constructor for class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Constructor for the RealImage3D object
reCalibrateObject() - Method in class mcib3d.geom.Object3DSurface
 
reCalibratePoints() - Method in class mcib3d.geom.Object3DSurface
 
RecShift() - Method in class mcib3d.ext.Imod
Description of the Method
RED - Variable in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
Description of the Field
reduce() - Method in class mcib3d.tracking_dev.HungarianAlgorithm
Reduce the cost matrix by subtracting the smallest element of each row from all elements of the row as well as the smallest element of each column from all elements of the column.
RegionGrowing - Class in mcib3d.image3d.regionGrowing
/** Copyright (C) 2008- 2012 Thomas Boudier and others This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
RegionGrowing(ImageHandler, ImageHandler, int, int) - Constructor for class mcib3d.image3d.regionGrowing.RegionGrowing
 
RegionGrowing(ImageStack, ImageStack, int, int) - Constructor for class mcib3d.image3d.regionGrowing.RegionGrowing
 
regular(float, float, float) - Method in class mcib3d.geom.Object3D
 
remain(int) - Method in class mcib3d.utils.Chrono
Description of the Method
remainingTimeEstimate(int) - Method in class mcib3d.utils.Chrono
 
remainString(int) - Method in class mcib3d.utils.Chrono
Description of the Method
removeAllChildren() - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
removeChild(ObjectTrack) - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
removeObject(int) - Method in class mcib3d.geom.Objects3DPopulation
 
removeObject(Object3D) - Method in class mcib3d.geom.Objects3DPopulation
 
RemoveObjectsBorder_ - Class in mcib_plugins
 
RemoveObjectsBorder_() - Constructor for class mcib_plugins.RemoveObjectsBorder_
 
removeObjectsTouchingBorders(ImageHandler, boolean) - Method in class mcib3d.geom.Objects3DPopulation
 
removeObjectsTouchingBorders(ImagePlus, boolean) - Method in class mcib3d.geom.Objects3DPopulation
 
removeValueAt(int) - Method in class mcib3d.utils.ArrayUtil
remove a value at a position
removeValues(double) - Method in class mcib3d.utils.ArrayUtil
 
removeVoxels(int) - Method in class mcib3d.geom.Object3DVoxels
 
REPLACE - Static variable in class mcib3d.image3d.processing.FastOperation3D
 
replacePixelsValue(int, int) - Method in class mcib3d.image3d.ImageHandler
Replace a pixel value by another
replacePixelsValue(int, int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
replacePixelsValue(int, int) - Method in class mcib3d.image3d.ImageInt
Replace a pixel value by another
replacePixelsValue(int, int, int, int) - Method in class mcib3d.image3d.ImageInt
Replace a pixel value by another
replacePixelsValue(int[], int[]) - Method in class mcib3d.image3d.ImageInt
Replace pixel values by others
replacePixelsValue(int[], int) - Method in class mcib3d.image3d.ImageInt
Replace a pixel values by another
replacePixelsValue(int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Replace a pixel value by another
replacePixelsValue(int, int, Object3DVoxels) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Replace a pixel value by another within a specified object
replaceRegion(int, int) - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
replaceRegion(int[], int) - Method in class mcib3d.image3d.regionGrowing.AllRegionsAssociation
 
replaceRegion(int, int) - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
 
resample(int, int, int, int) - Method in class mcib3d.image3d.BlankMask
 
resample(int, int) - Method in class mcib3d.image3d.BlankMask
 
resample(int, int, int, int) - Method in class mcib3d.image3d.ImageByte
 
resample(int, int) - Method in class mcib3d.image3d.ImageByte
Rescale the image to new dimension, only in Z
resample(int, int, int, int) - Method in class mcib3d.image3d.ImageFloat
 
resample(int, int) - Method in class mcib3d.image3d.ImageFloat
 
resample(int, int, int, int) - Method in class mcib3d.image3d.ImageHandler
Rescale the image to new dimension, in X Y and Z
resample(int, int) - Method in class mcib3d.image3d.ImageHandler
Rescale the image to new dimension, only in Z
resample(int, int, int, int) - Method in class mcib3d.image3d.ImageInt
 
resample(int, int) - Method in class mcib3d.image3d.ImageInt
Rescale the image to new dimension, only in Z
resample(int, int, int, int) - Method in class mcib3d.image3d.ImageShort
 
resample(int, int) - Method in class mcib3d.image3d.ImageShort
Rescale the image to new dimension, only in Z
resampleCdf(ArrayUtil, ArrayUtil, ArrayUtil) - Static method in class mcib3d.utils.CDFTools
 
reset() - Method in class mcib3d.align.Align2D
Description of the Method
reset() - Method in class mcib3d.geom.GeomTransform3D
Reset the matrix to identity
reset() - Method in class mcib3d.geom.Gradient
Reprend tout à zéro
reset() - Method in class mcib3d.geom.ObjectCreator3D
 
reset(int) - Method in class mcib3d.geom.ObjectCreator3D
 
reset() - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
set all pixels to 0
reset(float) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Reset the image to a given value
resetAi() - Method in class mcib3d.utils.ThreadRunner
 
resetColocalisation() - Method in class mcib3d.geom.Objects3DPopulationColocalisation
Reset the colocalisation In case some information changed in the populations
resetImage() - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Description of the Method
resetMinAndMax() - Method in class mcib3d.image3d.ImageStats
 
resetQuantifImage() - Method in class mcib3d.geom.Object3D
 
resetStats(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
resetStats() - Method in class mcib3d.image3d.ImageHandler
 
resize(int, int, int) - Method in class mcib3d.image3d.BlankMask
 
resize(int, int, int) - Method in class mcib3d.image3d.ImageByte
 
resize(int, int, int) - Method in class mcib3d.image3d.ImageFloat
 
resize(int, int, int) - Method in class mcib3d.image3d.ImageHandler
Enlarge the canvas size of the image in X, Y and Z .
resize(int, int, int) - Method in class mcib3d.image3d.ImageShort
 
restart(List<Point3f>) - Method in class mcib3d.geom.deformation3d.Mesh
 
ResultsFrame - Class in mcib_plugins.tools
 
ResultsFrame(String, String[], Object[][], RoiManager3D_2, int) - Constructor for class mcib_plugins.tools.ResultsFrame
 
ResultsFrame(String, String[], Object[][], int) - Constructor for class mcib_plugins.tools.ResultsFrame
 
ResultsTableModel - Class in mcib_plugins.tools
 
ResultsTableModel(String[], Object[][]) - Constructor for class mcib_plugins.tools.ResultsTableModel
 
resXY - Variable in class mcib3d.geom.Object3D
the resolution in XY
resZ - Variable in class mcib3d.geom.Object3D
the resolution in Z
reverse() - Method in class mcib3d.utils.ArrayUtil
 
RFA - Static variable in class mcib3d.align.Align3D
Description of the Field
RFilter() - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Description of the Method
RFilter(float, boolean) - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Filtre R pour tomographie sur FFT centree
RH_Maxima(int, int) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Méthode du RH maxima
RIGHT - Static variable in class mcib_plugins.Filter3D.Kernel3D
 
RoiManager3D_2 - Class in mcib_plugins.tools
 
RoiManager3D_2() - Constructor for class mcib_plugins.tools.RoiManager3D_2
Creates new form RoiManager3D_2
RoiManager3D_Options - Class in mcib_plugins.tools
 
RoiManager3D_Options() - Constructor for class mcib_plugins.tools.RoiManager3D_Options
 
rotate(Vector3D, double) - Method in class mcib3d.geom.Object3DSurface
 
rotate(Vector3D, double) - Method in class mcib3d.geom.Object3DVoxels
 
roughDisplacement(double) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
round(double, int) - Method in class mcib3d.image3d.processing.ImageColocalizer
 
run(ImagePlus) - Method in class mcib3d.image3d.distanceMap3d.CleanUpLocalThickness
Deprecated.
 
run(ImagePlus, float, float, int) - Method in class mcib3d.image3d.distanceMap3d.DistanceRidge
Deprecated.
 
run(ImageHandler, float, float, float, boolean, int) - Static method in class mcib3d.image3d.distanceMap3d.EDT
 
run(ImageHandler, float, boolean, int) - Static method in class mcib3d.image3d.distanceMap3d.EDT
 
run(ImageByte, int, float, float, int) - Method in class mcib3d.image3d.distanceMap3d.EdtByte
 
run(ImageByte, int, float, float, int) - Method in class mcib3d.image3d.distanceMap3d.EdtByteInv
 
run(ImageFloat, float, float, float, int) - Method in class mcib3d.image3d.distanceMap3d.EdtFloat
 
run(ImageFloat, float, float, float, int) - Method in class mcib3d.image3d.distanceMap3d.EdtFloatInv
 
run(ImageShort, int, float, float, int) - Method in class mcib3d.image3d.distanceMap3d.EdtShort
 
run(ImageShort, int, float, float, int) - Method in class mcib3d.image3d.distanceMap3d.EdtShortInv
 
run(ImageShort, float, float, int) - Method in class mcib3d.image3d.distanceMap3d.EdtShortLabel
 
run(ImagePlus, float, float, int) - Method in class mcib3d.image3d.distanceMap3d.LocalThickness
Deprecated.
 
run(String) - Method in class mcib3d.tracking_dev.Association_Track_Plugin
 
run(String) - Method in class mcib_plugins.About
 
run(String) - Method in class mcib_plugins.Association_
 
run(ImageProcessor) - Method in class mcib_plugins.Association_Tracking
 
run(ImageProcessor) - Method in class mcib_plugins.Binary_Close
 
run(ImageProcessor) - Method in class mcib_plugins.Binary_Interpolator
 
run(ImagePlus, Roi[]) - Method in class mcib_plugins.BinaryInterpolator
 
run(ImageStack) - Method in class mcib_plugins.BinaryInterpolator
 
run(ImageProcessor) - Method in class mcib_plugins.Canny_Symmetry
 
run() - Method in class mcib_plugins.ConnectionThresholding_
Main processing method for the ThresholdAdjuster object
run(ImageProcessor) - Method in class mcib_plugins.Convex_Hull3D
Main processing method for the plugin
run(ImageProcessor) - Method in class mcib_plugins.Crop3D_
Main processing method for the Crop3D_ object
run(ImageProcessor) - Method in class mcib_plugins.Crop3D_All
Main processing method for the Crop3D_ object
run(String) - Method in class mcib_plugins.Density3D_
 
run(String) - Method in class mcib_plugins.Distances_
 
run(String) - Method in class mcib_plugins.EDT_3D
 
run(ImageProcessor) - Method in class mcib_plugins.Ellipsoids_3D
Main processing method for the Axes3D_ object
run(String) - Method in class mcib_plugins.EVF_Radial
 
run(ImageProcessor) - Method in class mcib_plugins.Fast_filters3D
Main processing method for the Median3D_ object
run(String) - Method in class mcib_plugins.Fill_Holes3D
 
run(ImageProcessor) - Method in class mcib_plugins.Fill_Holes3D
 
run(ImageProcessor) - Method in class mcib_plugins.Filters3d_jni
Main processing method for the Median3D_ object
run(ImageProcessor) - Method in class mcib_plugins.Hysteresis_Thresholding
 
run(String) - Method in class mcib_plugins.Interactions_
 
run(String) - Method in class mcib_plugins.Line3D_
Main processing method for the Sphere3D_ object
run(ImageProcessor) - Method in class mcib_plugins.MaximaFinder3D_
 
run(String) - Method in class mcib_plugins.Mereo_3D
 
run(String) - Method in class mcib_plugins.Multi_Coloc
 
run(ImageProcessor) - Method in class mcib_plugins.Numbering_
 
run(String) - Method in class mcib_plugins.ObjectCreator_
Main processing method for the ObjectCreator_ object
run(String) - Method in class mcib_plugins.processing.Binary_Open
 
run(ImageProcessor) - Method in class mcib_plugins.Radial_3D
Main processing method for the Median3D_ object
run(ImageProcessor) - Method in class mcib_plugins.RDAR_
 
run(ImageProcessor) - Method in class mcib_plugins.RemoveObjectsBorder_
 
run(String) - Method in class mcib_plugins.SeedSpots_Plus
 
run(ImageProcessor) - Method in class mcib_plugins.Segment3D_
 
run(String) - Method in class mcib_plugins.segmentation.Manual_Spot
 
run(ImageProcessor) - Method in class mcib_plugins.segNuclei_
 
run(String) - Method in class mcib_plugins.Shape3D_
Main processing method for the Shape3D_ object
run(ImageProcessor) - Method in class mcib_plugins.Simple_Dist_Analysis
 
run(ImageProcessor) - Method in class mcib_plugins.Simple_MeasureCentroid
 
run(ImageProcessor) - Method in class mcib_plugins.Simple_MeasureGeometrical
 
run(ImageProcessor) - Method in class mcib_plugins.Simple_MeasureMesh
 
run(ImageProcessor) - Method in class mcib_plugins.Simple_MeasureShape
 
run(ImageProcessor) - Method in class mcib_plugins.Simple_MeasureStatistics
 
run(ImageProcessor) - Method in class mcib_plugins.Stats_Spat3D
Main processing method
run(String) - Method in class mcib_plugins.tools.Draw_RoiSlices
 
run(String) - Method in class mcib_plugins.tools.RoiManager3D_2
 
run(String) - Method in class mcib_plugins.tools.RoiManager3D_Options
 
run(ImageProcessor) - Method in class mcib_plugins.Track_Threshold
 
run(String) - Method in class mcib_plugins.Watershed_3D
 
run(String) - Method in class mcib_plugins.Watershed_Split3D
 
run(String) - Method in class mcib_plugins.Watershed_Voronoi3D
 
run_includeInside(ImageHandler, int, float, float, boolean, int) - Static method in class mcib3d.image3d.distanceMap3d.EDT
 
run_includeInside(ImageHandler, int, boolean, int) - Static method in class mcib3d.image3d.distanceMap3d.EDT
 
runCommand(String, boolean) - Method in class mcib3d.utils.Shell
Lancement de commandes
runCommand(String) - Method in class mcib3d.utils.Shell
 
runEdtLabel(ImageInt, float, float, int) - Static method in class mcib3d.image3d.distanceMap3d.EDT
 
runPostFilter(ImageInt) - Method in class mcib_plugins.Binary_Close
 
runPostFilter(ImageInt) - Method in class mcib_plugins.processing.Binary_Open
 

S

s - Variable in class mcib3d.image3d.distanceMap3d.CleanUpLocalThickness
Deprecated.
 
s002 - Variable in class mcib3d.geom.Object3D
 
s003 - Variable in class mcib3d.geom.Object3D
 
s004 - Variable in class mcib3d.geom.Object3D
 
s011 - Variable in class mcib3d.geom.Object3D
 
s012 - Variable in class mcib3d.geom.Object3D
 
s013 - Variable in class mcib3d.geom.Object3D
 
s020 - Variable in class mcib3d.geom.Object3D
 
s021 - Variable in class mcib3d.geom.Object3D
 
s022 - Variable in class mcib3d.geom.Object3D
 
s030 - Variable in class mcib3d.geom.Object3D
 
s031 - Variable in class mcib3d.geom.Object3D
 
s040 - Variable in class mcib3d.geom.Object3D
 
s101 - Variable in class mcib3d.geom.Object3D
 
s102 - Variable in class mcib3d.geom.Object3D
 
s103 - Variable in class mcib3d.geom.Object3D
 
s110 - Variable in class mcib3d.geom.Object3D
 
s111 - Variable in class mcib3d.geom.Object3D
 
s112 - Variable in class mcib3d.geom.Object3D
 
s120 - Variable in class mcib3d.geom.Object3D
 
s121 - Variable in class mcib3d.geom.Object3D
 
s130 - Variable in class mcib3d.geom.Object3D
 
s200 - Variable in class mcib3d.geom.Object3D
Centred Moments order 2
s201 - Variable in class mcib3d.geom.Object3D
 
s202 - Variable in class mcib3d.geom.Object3D
 
s210 - Variable in class mcib3d.geom.Object3D
 
s211 - Variable in class mcib3d.geom.Object3D
 
s220 - Variable in class mcib3d.geom.Object3D
 
s300 - Variable in class mcib3d.geom.Object3D
Centred Moments order 3
s301 - Variable in class mcib3d.geom.Object3D
 
s310 - Variable in class mcib3d.geom.Object3D
 
s400 - Variable in class mcib3d.geom.Object3D
Centred Moments order 4
sameDimensions(ImageHandler) - Method in class mcib3d.image3d.ImageHandler
 
sameDimensions(ImagePlus) - Method in class mcib3d.image3d.ImageHandler
 
sameDimentions(ImageHandler) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
sameDimentions(ImagePlus) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
samePosition(Point3D, double) - Method in class mcib3d.geom.Point3D
 
samePosition(Point3D) - Method in class mcib3d.geom.Point3D
 
sameVoxel(Point3D) - Method in class mcib3d.geom.Point3D
 
sameVoxel(Point3DInt) - Method in class mcib3d.geom.Point3D
 
sameVoxel(Point3DInt) - Method in class mcib3d.geom.Point3DInt
 
Sample() - Method in class mcib3d.ext.Imod
Description of the Method
save(String, boolean) - Method in class mcib3d.image3d.ImageHandler
 
save(String) - Method in class mcib3d.image3d.ImageHandler
 
saveArray(String, String, String) - Method in class mcib3d.utils.ArrayUtil
 
saveAsPngSequence(ImageHandler, String, String, int, int, boolean) - Static method in class mcib3d.image3d.ImagePlus_Utils
 
saveAsPngSequence(ImagePlus, String, String, int, int, boolean) - Static method in class mcib3d.image3d.ImagePlus_Utils
 
saveDatasetARFF(String) - Method in class mcib3d.Classification.DataSet
 
saveInfo(BufferedWriter) - Method in class mcib3d.geom.Object3D
 
saveObject(String) - Method in class mcib3d.geom.Object3D
 
saveObject(String) - Method in class mcib3d.geom.Object3DFuzzy
 
saveObject(String) - Method in class mcib3d.geom.Object3DLabel
 
saveObject(String) - Method in class mcib3d.geom.Object3DSurface
 
saveObject(String) - Method in class mcib3d.geom.Object3DVoxels
 
saveObjects(String) - Method in class mcib3d.geom.Objects3DPopulation
 
saveObjects(String, int[]) - Method in class mcib3d.geom.Objects3DPopulation
 
saveThumbNail(int, int, String) - Method in class mcib3d.image3d.ImageHandler
 
scale(double) - Method in class mcib3d.geom.Object3DSurface
 
scale(double, Vector3D) - Method in class mcib3d.geom.Object3DSurface
 
scale(double, double, double) - Method in class mcib3d.geom.Point3D
 
scale - Variable in class mcib3d.image3d.distanceMap3d.DistanceRidge
Deprecated.
 
scale - Variable in class mcib3d.image3d.distanceMap3d.LocalThickness
Deprecated.
 
scaleInv - Variable in class mcib3d.image3d.distanceMap3d.DistanceRidge
Deprecated.
 
scaleInv - Variable in class mcib3d.image3d.distanceMap3d.LocalThickness
Deprecated.
 
scaleInvSq - Variable in class mcib3d.image3d.distanceMap3d.DistanceRidge
Deprecated.
 
scaleInvSq - Variable in class mcib3d.image3d.distanceMap3d.LocalThickness
Deprecated.
 
scaleSq - Variable in class mcib3d.image3d.distanceMap3d.DistanceRidge
Deprecated.
 
scaleSq - Variable in class mcib3d.image3d.distanceMap3d.LocalThickness
Deprecated.
 
SDI(ArrayUtil, ArrayUtil[], ArrayUtil, ArrayUtil) - Static method in class mcib3d.utils.CDFTools
 
secondClosestCenter(Object3D, double) - Method in class mcib3d.geom.Objects3DPopulation
Get the second closest object in the population from given object with distance greater than given distance
secondClosestCenter(Object3D, boolean) - Method in class mcib3d.geom.Objects3DPopulation
Get the second closest object in the population from given object with distance greater than given distance
secondClosestCenter(Object3D, ArrayList<Object3D>) - Method in class mcib3d.geom.Objects3DPopulation
 
seed - Variable in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
SeedSpots_Plus - Class in mcib_plugins
Description of the Class
SeedSpots_Plus() - Constructor for class mcib_plugins.SeedSpots_Plus
 
SEG_BLOCK - Static variable in class mcib3d.image3d.Segment3DSpots
 
SEG_CLASSICAL - Static variable in class mcib3d.image3d.Segment3DSpots
 
SEG_MAX - Static variable in class mcib3d.image3d.Segment3DSpots
 
segment(ImageHandler, boolean) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
segment(ImagePlus, boolean) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
segment() - Method in class mcib3d.image3d.Segment3DImage
Generates the connexity analysis.
Segment3D_ - Class in mcib_plugins
* /** Copyright (C) 2008- 2012 Thomas Boudier and others
Segment3D_() - Constructor for class mcib_plugins.Segment3D_
 
Segment3DImage - Class in mcib3d.image3d
Description of the Class
Segment3DImage(ImageHandler, float, float) - Constructor for class mcib3d.image3d.Segment3DImage
Constructor for the Segment3DImage object
Segment3DImage(ImagePlus, float, float) - Constructor for class mcib3d.image3d.Segment3DImage
 
Segment3DSpots - Class in mcib3d.image3d
 
Segment3DSpots(ImageHandler, ImageHandler) - Constructor for class mcib3d.image3d.Segment3DSpots
 
segmentAll(ImageHandler, boolean) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
segmentAll() - Method in class mcib3d.image3d.Segment3DSpots
 
segmentBest(ImageHandler, boolean) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
segmentBest(ImagePlus, boolean) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
segmentOneSpot(int, int, int, int) - Method in class mcib3d.image3d.Segment3DSpots
 
segmentSpotBlock(int, int, int, int, int) - Method in class mcib3d.image3d.Segment3DSpots
 
segmentSpotClassical(int, int, int, int, int) - Method in class mcib3d.image3d.Segment3DSpots
Segment an object from a seed
segmentSpotMax(int, int, int, int, int) - Method in class mcib3d.image3d.Segment3DSpots
Segment an object from a seed, keep only max local
SegNuclei - Class in mcib_plugins.segmentation
Created by thomasb on 22/8/16.
SegNuclei(ImageInt, ImageInt) - Constructor for class mcib_plugins.segmentation.SegNuclei
 
segNuclei_ - Class in mcib_plugins
 
segNuclei_() - Constructor for class mcib_plugins.segNuclei_
 
selectByName(String) - Method in class mcib_plugins.tools.RoiManager3D_2
 
selectByNames(String[]) - Method in class mcib_plugins.tools.RoiManager3D_2
 
selectByNumber(int) - Method in class mcib_plugins.tools.RoiManager3D_2
 
selectByNumbers(int[]) - Method in class mcib_plugins.tools.RoiManager3D_2
 
selectFor(int, int, int) - Method in class mcib_plugins.tools.RoiManager3D_2
 
selection - Variable in class mcib3d.align.Align2D
Description of the Field
separatedBorder(int, int) - Method in class mcib3d.geom.Objects3DPopulationAnalysis
Deprecated.
 
separatedCenter(int, int) - Method in class mcib3d.geom.Objects3DPopulationAnalysis
Deprecated.
 
set(int, int, double) - Method in class mcib3d.Jama.Matrix
Set a single element.
set332RGBLut() - Method in class mcib3d.image3d.ImageHandler
 
setA(Object3D) - Method in class mcib3d.geom.MereoObject3D
 
setAddAngles(float) - Method in class mcib3d.ext.ImodConf
Sets the addAngles attribute of the ImodConf object
setAdjTriangles(ArrayList<Integer>) - Method in class mcib3d.geom.deformation3d.Vertex
 
setAlpha(double) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
setAlpha(double) - Method in class mcib3d.image3d.processing.CannyDeriche1D
 
setAlpha(double) - Method in class mcib3d.image3d.processing.CannyEdge3D
 
setAlphas(double[]) - Method in class mcib3d.geom.Gradient
Définir la transparence des pixels limites
setAngleDebut(float) - Method in class mcib3d.ext.ImodConf
Sets the angleDebut attribute of the ImodConf object
setAngleDebut(float) - Method in class mcib3d.ext.XmippConf
Sets the angleDebut attribute of the XmippConf object
setAngleFin(float) - Method in class mcib3d.ext.XmippConf
Sets the angleFin attribute of the XmippConf object
setAngleIncrement(float) - Method in class mcib3d.ext.ImodConf
Sets the angleIncrement attribute of the ImodConf object
setAngleIncrement(float) - Method in class mcib3d.ext.XmippConf
Sets the angleIncrement attribute of the XmippConf object
setAnim(boolean) - Method in class mcib3d.image3d.regionGrowing.Watershed3D
 
setB(Object3D) - Method in class mcib3d.geom.MereoObject3D
 
setBille(int) - Method in class mcib3d.ext.ImodConf
Sets the bille attribute of the ImodConf object
setBins(double[]) - Method in class mcib3d.utils.HistogramUtil
 
setCalibration(Calibration) - Method in class mcib3d.geom.Object3D
Deprecated.
use Object3D-IJUtils Sets the calibration of the Object3D (ImageJ)
setCalibration(double, double, String) - Method in class mcib3d.geom.Object3D
Sets the calibration of the Object3D
setCalibration(Object3D, Calibration) - Static method in class mcib3d.geom.Object3D_IJUtils
 
setCalibration(Calibration) - Method in class mcib3d.geom.ObjectCreator3D
Sets the calibration attribute of the Object3D object
setCalibration(Calibration) - Method in class mcib3d.geom.Objects3DPopulation
Deprecated.
setCalibration(double, double, String) - Method in class mcib3d.geom.Objects3DPopulation
 
setCalibration(Calibration) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
setCenter(Vector3D) - Method in class mcib3d.geom.Gradient
Définir le centre du gradient.
setCenter(Point3D) - Method in class mcib3d.geom.Gradient
Définir le centre du gradient.
setCenter(boolean) - Method in class mcib3d.image3d.legacy.FHTImage3D
Deprecated.
Sets the center attribute of the FHTImage3D object
setClass(int) - Method in class mcib3d.Classification.Data
 
setColocMitosis(double) - Method in class mcib3d.tracking_dev.Mitosis
 
setColor(IntImage3D, String) - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
met une couleur donnee a l'image3D
setColor(ImageStack, String) - Method in class mcib3d.image3d.legacy.ColorImage3D
Deprecated.
met une couleur donnee a l'image3D
setColorsPlot(Color, Color, Color) - Method in class mcib3d.spatial.analysis.SpatialStatistics
 
setColorsPlot(Color, Color, Color) - Method in class mcib_plugins.analysis.spatialAnalysis
 
setComment(String) - Method in class mcib3d.geom.Object3D
 
setConcat(boolean) - Method in class mcib3d.utils.Logger.TextLog
 
setConf(ImodConf) - Method in class mcib3d.ext.Imod
Sets the conf attribute of the Imod object
setConf(XmippConf) - Method in class mcib3d.ext.Xmipp
Sets the conf attribute of the Xmipp object
setContours(LinkedList<Voxel3D>) - Method in class mcib3d.geom.Object3DFuzzy
 
setContours(LinkedList<Voxel3D>, double) - Method in class mcib3d.geom.Object3DVoxels
 
setCoord(double, double, double) - Method in class mcib3d.geom.Vector3D
Sets the attributes of the Vector3D object
setCoord(int) - Method in class mcib3d.image3d.Coordinate3D
 
setCoord(int, int, int, int) - Method in class mcib3d.image3d.Coordinate3D
 
setCoord(int, int, int) - Method in class mcib3d.image3d.Coordinate3D
 
setCoordRandom() - Method in class mcib3d.geom.Point3D
set coordinates with random numbers between -1 and 1
setCoordRandom() - Method in class mcib3d.geom.Vector3D
 
setCriteriaMethod(int) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
setCurrentObject(Object3D) - Method in class mcib3d.geom.ObjectsPopulationDistances
 
setDifferenceKernel(int) - Method in class mcib_plugins.Filter3D.Kernel3D
 
setDistMax(double) - Method in class mcib3d.tracking_dev.CostColocalisation
 
setEdges(ImageHandler[]) - Method in class mcib3d.image3d.processing.SymmetryFilter
 
setEnvelope(double) - Method in class mcib3d.spatial.analysis.SpatialStatistics
 
setEraser(boolean) - Method in class mcib3d.ext.ImodConf
Sets the eraser attribute of the ImodConf object
setExclure(String) - Method in class mcib3d.ext.ImodConf
Sets the exclure attribute of the ImodConf object
setFastButLessAccurate(boolean) - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
 
setFilter(int) - Method in class mcib_plugins.Fast_filters3D
 
setFrame(int) - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
setGaussMaxr(int) - Method in class mcib3d.image3d.Segment3DSpots
 
setGaussPc(double) - Method in class mcib3d.image3d.Segment3DSpots
 
setGraysLut() - Method in class mcib3d.image3d.ImageHandler
 
setHisto256(int[], double) - Method in class mcib3d.image3d.ImageStats
 
setId(int) - Method in class mcib3d.geom.deformation3d.Vertex
 
setImage(ImageHandler) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
setImage(ImageHandler) - Method in class mcib3d.image3d.processing.MaximaFinder
A new image to process
setImage1(ImageHandler) - Method in class mcib3d.tracking_dev.TrackingAssociation
 
setImage2(ImageHandler) - Method in class mcib3d.tracking_dev.TrackingAssociation
 
setImageMarkers(ImageInt) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
setImageZones(ImageInt) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
setImproved(boolean) - Method in class mcib3d.image3d.processing.SymmetryFilter
 
setInput(ImageHandler) - Method in class mcib3d.image3d.processing.CannyEdge3D
 
setInteractions(InteractionsList) - Method in class mcib3d.tracking_dev.CostPairMitosis
 
setIteration(int) - Method in class mcib3d.ext.XmippConf
Sets the iteration attribute of the XmippConf object
setLabel(double) - Method in class mcib3d.geom.Voxel3DComparable
 
setLabel(int) - Method in class mcib3d.image3d.ImageLabeller.Spot3D
 
setLabel(int) - Method in class mcib3d.image3d.ImageLabeller.Vox3D
 
setLabel(int) - Method in class mcib3d.image3d.ImageLabeller2D.Spot2D
 
setLabel(int) - Method in class mcib3d.image3d.ImageLabeller2D.Vox2D
 
setLabelImage(ImageInt) - Method in class mcib3d.geom.Object3D
Sets the label image of the object (should start at 0,0,0)
setLabelImage(ImageHandler) - Method in class mcib3d.image3d.Segment3DSpots
 
setLabelSeeds(boolean) - Method in class mcib3d.image3d.regionGrowing.Watershed3D
 
setLabelSeeds(boolean) - Method in class mcib3d.image3d.regionGrowing.Watershed3DVoronoi
 
setLine(double[]) - Method in class mcib3d.geom.deformation3d.Deriche
 
setLine(double[]) - Method in class mcib3d.image3d.processing.CannyDeriche1D
 
setLineX(int, int, int, double[]) - Method in class mcib3d.image3d.ImageHandler
 
setLineY(int, int, int, double[]) - Method in class mcib3d.image3d.ImageHandler
 
setLineZ(int, int, int, double[]) - Method in class mcib3d.image3d.ImageHandler
 
setLocalDiff(int) - Method in class mcib3d.image3d.Segment3DSpots
 
setLocalThreshold(int) - Method in class mcib3d.image3d.Segment3DSpots
 
setLog(AbstractLog) - Method in class mcib3d.geom.MereoAnalysis
 
setLog(AbstractLog) - Method in class mcib3d.geom.Objects3DPopulation
 
setLog(AbstractLog) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
setLog(AbstractLog) - Method in class mcib3d.image3d.regionGrowing.Watershed3D
 
setLog(AbstractLog) - Method in class mcib3d.image3d.regionGrowing.Watershed3DVoronoi
 
setManager(RoiManager3D_2) - Method in class mcib_plugins.tools.ResultsFrame
 
setMarker(boolean) - Method in class mcib3d.geom.deformation3d.Vertex
 
setMarkers(ArrayList<Point3D>) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
setMask(Object3D) - Method in class mcib3d.geom.Objects3DPopulation
 
setMatrix(int, int, int, int, Matrix) - Method in class mcib3d.Jama.Matrix
Set a submatrix.
setMatrix(int[], int[], Matrix) - Method in class mcib3d.Jama.Matrix
Set a submatrix.
setMatrix(int[], int, int, Matrix) - Method in class mcib3d.Jama.Matrix
Set a submatrix.
setMatrix(int, int, int[], Matrix) - Method in class mcib3d.Jama.Matrix
Set a submatrix.
setMax(int, int) - Method in class mcib3d.geom.Voxel3DComparable
 
setMaxCost(double) - Method in class mcib3d.tracking_dev.CostPairMitosis
 
setMaxCost(double) - Method in class mcib3d.tracking_dev.CostTouching
 
setMaxDistance(int) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
setMaxsize(int) - Method in class mcib3d.image3d.ImageLabeller
 
setMaxsize(int) - Method in class mcib3d.image3d.ImageLabeller2D
 
setMaxSizeObject(int) - Method in class mcib3d.image3d.Segment3DImage
 
setMerge(boolean) - Method in class mcib3d.tracking_dev.TrackingAssociation
 
setMethod(int) - Method in class mcib3d.geom.Objects3DPopulationInteractions
 
setMethodLocal(int) - Method in class mcib3d.image3d.Segment3DSpots
 
setMethodSeg(int) - Method in class mcib3d.image3d.Segment3DSpots
 
setMethodThreshold(int) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
setMinAndMax(ImageInt) - Method in class mcib3d.image3d.BlankMask
 
setMinAndMax(ImageInt) - Method in class mcib3d.image3d.ImageHandler
 
setMinAndMax(float, float) - Method in class mcib3d.image3d.ImageHandler
 
setMinAndMax(double, double) - Method in class mcib3d.image3d.ImageStats
 
setMinColoc(double) - Method in class mcib3d.tracking_dev.CostPairMitosis
 
setMinColocMitosis(double) - Method in class mcib3d.tracking_dev.MitosisDetector
 
setMinSize(int) - Method in class mcib3d.image3d.ImageLabeller
 
setMinSize(int) - Method in class mcib3d.image3d.ImageLabeller2D
 
setMinSizeObject(int) - Method in class mcib3d.image3d.Segment3DImage
 
setMitosis(boolean) - Method in class mcib3d.tracking_dev.TrackingAssociation
 
setMoments(double, double, double) - Method in class mcib3d.image3d.ImageStats
 
setMother(Object3D) - Method in class mcib3d.tracking_dev.Mitosis
 
setMultiThread(int) - Method in class mcib_plugins.analysis.spatialAnalysis
 
setName(String) - Method in class mcib3d.geom.Object3D
Sets the name
setNbCpus(int) - Method in class mcib3d.image3d.processing.MaximaFinder
Number of Cpus
setNbCpus(int) - Method in class mcib_plugins.Fast_filters3D
 
setNewCenter(double, double, double) - Method in class mcib3d.geom.Object3D
 
setNewCenter(Object3D) - Method in class mcib3d.geom.Object3D
 
setNewCenter(Vector3D) - Method in class mcib3d.geom.Object3D
 
setNoiseTolerance(float) - Method in class mcib3d.image3d.processing.MaximaFinder
The noise tolerance
setNoiseWatershed(int) - Method in class mcib3d.image3d.Segment3DSpots
Deprecated.
setNomSerie(String) - Method in class mcib3d.ext.ImodConf
Sets the nomSerie attribute of the ImodConf object
setNomSerie(String) - Method in class mcib3d.ext.XmippConf
Sets the nomSerie attribute of the XmippConf object
setNormalize(double) - Method in class mcib3d.image3d.processing.SymmetryFilter
 
setObject(int, Object3D) - Method in class mcib3d.geom.Objects3DPopulation
 
setObject3D(Object3D) - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
setOffset(ImageHandler) - Method in class mcib3d.image3d.ImageHandler
 
setOffset(int, int, int) - Method in class mcib3d.image3d.ImageHandler
 
setParent(ObjectTrack) - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
setPathImage(ImageHandler) - Method in class mcib3d.tracking_dev.TrackingAssociation
 
setPix(int, int, int, double) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
Sets the voxel value
setPix(int, int, int, double) - Method in class mcib3d.image3d.legacy.IntImage3D
Deprecated.
Sets the pix attribute of the IntImage3D object
setPix(int, int, int, double) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Sets the pixel value at position (x,y,z) as a double
setPixel(int, float) - Method in class mcib3d.image3d.BlankMask
 
setPixel(int, int, int, float) - Method in class mcib3d.image3d.BlankMask
 
setPixel(int, int, float) - Method in class mcib3d.image3d.BlankMask
 
setPixel(int, float) - Method in class mcib3d.image3d.ImageByte
Deprecated.
setPixel(Point3D, float) - Method in class mcib3d.image3d.ImageByte
 
setPixel(int, int, int, float) - Method in class mcib3d.image3d.ImageByte
 
setPixel(int, int, float) - Method in class mcib3d.image3d.ImageByte
 
setPixel(int, int, int, int) - Method in class mcib3d.image3d.ImageByte
 
setPixel(int, int, int) - Method in class mcib3d.image3d.ImageByte
 
setPixel(int, float) - Method in class mcib3d.image3d.ImageFloat
Deprecated.
setPixel(Point3D, float) - Method in class mcib3d.image3d.ImageFloat
 
setPixel(int, int, int, float) - Method in class mcib3d.image3d.ImageFloat
 
setPixel(int, int, float) - Method in class mcib3d.image3d.ImageFloat
 
setPixel(int, float) - Method in class mcib3d.image3d.ImageHandler
Deprecated.
setPixel(Point3D, float) - Method in class mcib3d.image3d.ImageHandler
 
setPixel(int, int, int, float) - Method in class mcib3d.image3d.ImageHandler
 
setPixel(int, int, float) - Method in class mcib3d.image3d.ImageHandler
 
setPixel(int, int, int, int) - Method in class mcib3d.image3d.ImageInt
 
setPixel(int, int, int) - Method in class mcib3d.image3d.ImageInt
 
setPixel(int, float) - Method in class mcib3d.image3d.ImageShort
Deprecated.
setPixel(Point3D, float) - Method in class mcib3d.image3d.ImageShort
 
setPixel(int, int, int, float) - Method in class mcib3d.image3d.ImageShort
 
setPixel(int, int, float) - Method in class mcib3d.image3d.ImageShort
 
setPixel(int, int, int, int) - Method in class mcib3d.image3d.ImageShort
 
setPixel(int, int, int) - Method in class mcib3d.image3d.ImageShort
 
setPixel(Voxel3D, short) - Method in class mcib3d.image3d.ImageShort
Set the pixel value at a given Voxel3D position (position will be rounded)
setPixelCross3D(int, int, int, int) - Method in class mcib3d.image3d.ImageByte
 
setPixelCross3D(int, int, int, int) - Method in class mcib3d.image3d.ImageInt
 
setPixelCross3D(int, int, int, int) - Method in class mcib3d.image3d.ImageShort
 
setPixelIncrement(int, int, int, float) - Method in class mcib3d.image3d.ImageHandler
 
setPixelIncrement(Point3D, float) - Method in class mcib3d.image3d.ImageHandler
 
setPoint(double, double, double) - Method in class mcib3d.geom.GradientPoint
 
setPopA(Objects3DPopulation) - Method in class mcib3d.geom.MereoAnalysis
 
setPopB(Objects3DPopulation) - Method in class mcib3d.geom.MereoAnalysis
 
setPopulation(Objects3DPopulation) - Method in class mcib3d.geom.ObjectsPopulationDistances
 
setPopulation(Objects3DPopulation) - Method in class mcib_plugins.segmentation.SegNuclei
 
setPosition(Point3f) - Method in class mcib3d.geom.deformation3d.Vertex
 
setRadii(float, float) - Method in class mcib3d.image3d.processing.MaximaFinder
The radii to compute local maxima
setRadius(int) - Method in class mcib3d.image3d.processing.SymmetryFilter
 
setRadiusLocalMean(float, float, float) - Method in class mcib3d.image3d.Segment3DSpots
 
setRadiusLocalMean(float, float, float, double) - Method in class mcib3d.image3d.Segment3DSpots
 
setRadiusMax(float) - Method in class mcib3d.image3d.regionGrowing.Watershed3DVoronoi
 
setRadiusXYPix(int) - Method in class mcib_plugins.Fast_filters3D
 
setRadiusZPix(int) - Method in class mcib_plugins.Fast_filters3D
 
setRadX(float) - Method in class mcib3d.geom.MereoAnalysis
 
setRadX(float) - Method in class mcib3d.geom.MereoObject3D
 
setRadxyForDilateMethod(float) - Method in class mcib3d.geom.Objects3DPopulationInteractions
 
setRadY(float) - Method in class mcib3d.geom.MereoAnalysis
 
setRadY(float) - Method in class mcib3d.geom.MereoObject3D
 
setRadZ(float) - Method in class mcib3d.geom.MereoAnalysis
 
setRadZ(float) - Method in class mcib3d.geom.MereoObject3D
 
setRadzForDilateMethod(float) - Method in class mcib3d.geom.Objects3DPopulationInteractions
 
setRatios(double[]) - Method in class mcib3d.geom.Gradient
Définir le ratio des pixels limites
setRawImage(ImageHandler) - Method in class mcib3d.image3d.regionGrowing.Watershed3D
Sets the raw image
setRawImage(ImageHandler) - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
Sets the raw image
setRawImage(ImageHandler) - Method in class mcib3d.image3d.Segment3DSpots
 
setRec(int) - Method in class mcib3d.ext.XmippConf
Sets the rec attribute of the XmippConf object
setRepertoireScripts(String) - Method in class mcib3d.ext.Imod
Sets the repertoireScripts attribute of the ImodConf object
setRepertoireTmp(String) - Method in class mcib3d.ext.Imod
Sets the repertoireTmp attribute of the ImodConf object
setResolution(double, double, String) - Method in class mcib3d.geom.ObjectCreator3D
Sets the resolution attribute of the ObjectCreator3D object
setResXY(double) - Method in class mcib3d.geom.Object3D
Sets the calibration in XY of the Object3D
setResZ(double) - Method in class mcib3d.geom.Object3D
Sets the calibration in Z of the Object3D
setRoi(Roi) - Method in class mcib3d.align.Align2D
Sets the roi attribute of the Align2D object
setRotation(int, double) - Method in class mcib3d.align.Align2D
Sets the rotation attribute of the Align2D object
setRotation(double, double, double) - Method in class mcib3d.geom.GeomTransform3D
Sets the rotation attribute of the Transform3D object
setRotation(Vector3D, double) - Method in class mcib3d.geom.GeomTransform3D
Sets the rotation around an axis with an angle
setRotationDegrees(double, double, double) - Method in class mcib3d.geom.GeomTransform3D
Sets the rotation attribute of the Transform3D object
setRotationXAxis(double) - Method in class mcib3d.geom.GeomTransform3D
Sets the rotation on the X Axis for the Transform
setRotationYAxis(double) - Method in class mcib3d.geom.GeomTransform3D
Sets the rotation on the Y Axis for the Transform
setRotationZAxis(double) - Method in class mcib3d.geom.GeomTransform3D
Sets the rotationZAxis attribute of the Transform3D object
setScale(double, double, double) - Method in class mcib3d.geom.GeomTransform3D
Scale factor
setScale(double, double, String) - Method in class mcib3d.geom.Objects3DPopulation
 
setScale(double, double, String) - Method in class mcib3d.image3d.ImageHandler
 
setScale(ImageHandler) - Method in class mcib3d.image3d.ImageHandler
 
setScale(double[]) - Method in class mcib3d.utils.KDTreeC
 
setScale3(double, double, double) - Method in class mcib3d.utils.KDTreeC
 
setScaleXY(double) - Method in class mcib3d.geom.Objects3DPopulation
 
setScaleZ(double) - Method in class mcib3d.geom.Objects3DPopulation
 
setScaling(double) - Method in class mcib3d.image3d.processing.SymmetryFilter
 
setSeeds(ImageInt) - Method in class mcib3d.image3d.regionGrowing.Watershed3D
set the seeds image used
setSeeds(ImageInt) - Method in class mcib3d.image3d.regionGrowing.Watershed3D_old
set the seeds iamge used
setSeeds(ImageInt) - Method in class mcib3d.image3d.regionGrowing.Watershed3DVoronoi
 
setSeeds(ImageInt) - Method in class mcib3d.image3d.Segment3DSpots
 
setSeedsThreshold(int) - Method in class mcib3d.image3d.Segment3DSpots
 
setShiftY(float) - Method in class mcib3d.ext.ImodConf
Sets the shiftY attribute of the ImodConf object
setShow(boolean) - Method in class mcib3d.image3d.processing.MaximaFinder
Deprecated.
setShowStatus(boolean) - Method in class mcib3d.geom.Object3DVoxels
 
setShowStatus(boolean) - Method in class mcib3d.image3d.legacy.Image3D
Deprecated.
 
setSize(int) - Method in class mcib3d.utils.ArrayUtil
new size of the array (can incresase size of array)
setSizes(int, int, int) - Method in class mcib3d.image3d.legacy.RealImage3D
Deprecated.
Sets the sizes attribute of the RealImage3D object
setSmooth_method(int) - Method in class mcib3d.geom.Object3DSurface
 
setSmoothingFactor(float) - Method in class mcib3d.geom.Object3DSurface
 
setSpherical() - Method in class mcib_plugins.Filter3D.Kernel3D
 
setStack(ImageStack) - Method in class mcib3d.align.Align2D
Sets the images to work with
setStack(ImageStack) - Method in class mcib3d.geom.deformation3d.Deriche
 
setState(int) - Method in class mcib3d.image3d.IterativeThresholding.ObjectTrack
 
setStep(int) - Method in class mcib3d.image3d.IterativeThresholding.BestCriteriaStable
 
setStopThreshold(int) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
setTailleX(int) - Method in class mcib3d.ext.XmippConf
Sets the tailleX attribute of the XmippConf object
setTailleY(int) - Method in class mcib3d.ext.XmippConf
Sets the tailleY attribute of the XmippConf object
setThickness(int) - Method in class mcib3d.ext.ImodConf
Sets the thickness attribute of the ImodConf object
setThresholdMax(double) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
setThresholdMin(double) - Method in class mcib3d.geom.deformation3d.DeformableMesh
 
setTiltAngle(float) - Method in class mcib3d.ext.ImodConf
Sets the tiltAngle attribute of the ImodConf object
setTiltAxis(float) - Method in class mcib3d.ext.XmippConf
Sets the tiltAxis attribute of the XmippConf object
setTitle(String) - Method in class mcib3d.image3d.ImageHandler
 
setTransform(double, double, double, double, double, double) - Method in class mcib3d.geom.GeomTransform3D
Sets a new transformation
setTransformation(GeomTransform3D) - Method in class mcib3d.geom.Gradient
Définir la matrice de transformation
setTransition(int) - Method in class mcib3d.geom.Gradient
Définir le type de transition
setTranslation(int, int, int) - Method in class mcib3d.align.Align2D
Sets the translation attribute of the Align2D object
setTranslation(double, double, double) - Method in class mcib3d.geom.GeomTransform3D
Sets the translation attribute of the Transform
setTx(int, int) - Method in class mcib3d.align.Align2D
Gets the translation on X Axis for an image
setTy(int, int) - Method in class mcib3d.align.Align2D
Gets the translation on Y Axis for an image
setType(int) - Method in class mcib3d.geom.Object3D
Sets the type
setUnit(String) - Method in class mcib3d.geom.Objects3DPopulation
 
setUnits(String) - Method in class mcib3d.geom.Object3D
Sets the units attribute for the calibration
setup(String, ImagePlus) - Method in class mcib_plugins.Association_Tracking
 
setup(String, ImagePlus) - Method in class mcib_plugins.Binary_Close
 
setup(String, ImagePlus) - Method in class mcib_plugins.Binary_Interpolator
 
setup(String, ImagePlus) - Method in class mcib_plugins.Canny_Symmetry
 
setup(String, ImagePlus) - Method in class mcib_plugins.Convex_Hull3D
 
setup(String, ImagePlus) - Method in class mcib_plugins.Crop3D_
Description of the Method
setup(String, ImagePlus) - Method in class mcib_plugins.Crop3D_All
Description of the Method
setup(String, ImagePlus) - Method in class mcib_plugins.Ellipsoids_3D
Description of the Method
setup(String, ImagePlus) - Method in class mcib_plugins.Fast_filters3D
setup
setup(String, ImagePlus) - Method in class mcib_plugins.Fill_Holes3D
 
setup(String, ImagePlus) - Method in class mcib_plugins.Filters3d_jni
setup
setup(String, ImagePlus) - Method in class mcib_plugins.Hysteresis_Thresholding
 
setup(String, ImagePlus) - Method in class mcib_plugins.MaximaFinder3D_
 
setup(String, ImagePlus) - Method in class mcib_plugins.Numbering_
 
setup(String, ImagePlus) - Method in class mcib_plugins.Radial_3D
Description of the Method
setup(String, ImagePlus) - Method in class mcib_plugins.RDAR_
 
setup(String, ImagePlus) - Method in class mcib_plugins.RemoveObjectsBorder_
 
setup(String, ImagePlus) - Method in class mcib_plugins.Segment3D_
 
setup(String, ImagePlus) - Method in class mcib_plugins.segNuclei_
 
setup(String, ImagePlus) - Method in class mcib_plugins.Simple_Dist_Analysis
 
setup(String, ImagePlus) - Method in class mcib_plugins.Simple_MeasureCentroid
 
setup(String, ImagePlus) - Method in class mcib_plugins.Simple_MeasureGeometrical
 
setup(String, ImagePlus) - Method in class mcib_plugins.Simple_MeasureMesh
 
setup(String, ImagePlus) - Method in class mcib_plugins.Simple_MeasureShape
 
setup(String, ImagePlus) - Method in class mcib_plugins.Simple_MeasureStatistics
 
setup(String, ImagePlus) - Method in class mcib_plugins.Stats_Spat3D
Description of the Method
setup(String, ImagePlus) - Method in class mcib_plugins.Track_Threshold
 
setUpdate(boolean) - Method in class mcib3d.utils.Logger.IJLog
 
setUse32bits(boolean) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
 
setValue(String, double) - Method in class mcib3d.Classification.Data<