- 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
- 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
-
- 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
-
- 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
-
- 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
- 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
-
- 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
-
- 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
- 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 - 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
-
- 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
-
- setValue(int) - Method in class mcib3d.geom.Object3D
-
Sets the value attribute of the Object3D object
- setValue(double) - Method in class mcib3d.geom.Voxel3D
-
- setValueAt(Object, int, int) - Method in class mcib_plugins.tools.ResultsTableModel
-
- setValues(int[]) - Method in class mcib3d.geom.Gradient
-
Définir la valeur des pixels limites.
- setValues(ArrayUtil) - Method in class mcib3d.utils.ArrayUtil
-
put values inside an array
- setVectorPoint3f(Point3f) - Method in class mcib3d.geom.Vector3D
-
Conctruct a vector from two points
- setVectorTwoPoint3f(Point3f, Point3f) - Method in class mcib3d.geom.Vector3D
-
- setVerbose(boolean) - Method in class mcib3d.image3d.IterativeThresholding.TrackThreshold
-
Deprecated.
- setVerbose(boolean) - Method in class mcib3d.image3d.processing.MaximaFinder
-
Display information
- setVerbose(boolean) - Method in class mcib3d.spatial.analysis.SpatialStatistics
-
- setVertices(Integer, Integer, Integer) - Method in class mcib3d.geom.deformation3d.Triangle
-
- setVois(float, float) - Method in class mcib3d.image3d.Coordinate3D
-
- setVois(float, float) - Method in class mcib3d.image3d.MaskIterator
-
Deprecated.
- setVois1(float) - Method in class mcib3d.image3d.Coordinate3D
-
- setVolume(Object3DVoxels) - Method in class mcib3d.geom.RDAR
-
- setVolumeMax(int) - Method in class mcib3d.image3d.Segment3DSpots
-
- setVolumeMin(int) - Method in class mcib3d.image3d.Segment3DSpots
-
- setVoxel(int, int, int, float) - Method in class mcib3d.geom.Voxel3D
-
Sets the pixel attribute of the Voxel3D object
- setVoxel(int, int, int, double) - Method in class mcib3d.geom.Voxel3D
-
Sets the pixel attribute of the Voxel3D object
- setVoxel(double, double, double, double) - Method in class mcib3d.geom.Voxel3D
-
- setVoxels(LinkedList<Voxel3D>) - Method in class mcib3d.geom.Object3DVoxels
-
- setWatershed(boolean) - Method in class mcib3d.image3d.Segment3DSpots
-
- setX(double) - Method in class mcib3d.geom.Point3D
-
Set the value of x
- setY(double) - Method in class mcib3d.geom.Point3D
-
Set the value of y
- setYnumber(double[]) - Method in class mcib3d.utils.HistogramUtil
-
- setZ(double) - Method in class mcib3d.geom.Point3D
-
Set the value of z
- Shape3D_ - Class in mcib_plugins
-
Description of the Class
- Shape3D_() - Constructor for class mcib_plugins.Shape3D_
-
- Shell - Class in mcib3d.utils
-
Interface avec le shell (lancement de commandes)
- Shell() - Constructor for class mcib3d.utils.Shell
-
- shiftIndexes(TreeMap<Integer, int[]>) - Method in class mcib3d.image3d.BlankMask
-
- shiftIndexes(TreeMap<Integer, int[]>) - Method in class mcib3d.image3d.ImageByte
-
- shiftIndexes(TreeMap<Integer, int[]>) - Method in class mcib3d.image3d.ImageInt
-
- shiftIndexes(TreeMap<Integer, int[]>) - Method in class mcib3d.image3d.ImageShort
-
- SHORT - Static variable in class mcib3d.image3d.legacy.Image3D
-
Deprecated.
SHORT
- show - Variable in class mcib3d.align.Align2D
-
Description of the Field
- show() - Method in class mcib3d.image3d.ImageHandler
-
- show(String) - Method in class mcib3d.image3d.ImageHandler
-
- show - Variable in class mcib3d.image3d.Segment3DSpots
-
- showDuplicate(String) - Method in class mcib3d.image3d.ImageHandler
-
- showFrame() - Method in class mcib_plugins.tools.ResultsFrame
-
- showInIJ(boolean) - Method in class mcib3d.align.Align2D
-
shows progress of computing in the status bar of ImageJ
- showStatus - Variable in class mcib3d.image3d.legacy.Image3D
-
Deprecated.
- shuffle() - Method in class mcib3d.geom.Objects3DPopulation
-
- shuffle() - Method in class mcib3d.utils.ArrayUtil
-
random mix of the values
- sigma(int, double) - Method in class mcib3d.align.Align2D
-
Description of the Method
- sigma - Variable in class mcib3d.geom.Object3D
-
standard deviation
- Simple_Dist_Analysis - Class in mcib_plugins
-
- Simple_Dist_Analysis() - Constructor for class mcib_plugins.Simple_Dist_Analysis
-
- Simple_MeasureCentroid - 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.
- Simple_MeasureCentroid() - Constructor for class mcib_plugins.Simple_MeasureCentroid
-
- Simple_MeasureGeometrical - Class in mcib_plugins
-
*
/**
Copyright (C) 2008- 2012 Thomas Boudier and others
- Simple_MeasureGeometrical() - Constructor for class mcib_plugins.Simple_MeasureGeometrical
-
- Simple_MeasureMesh - 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.
- Simple_MeasureMesh() - Constructor for class mcib_plugins.Simple_MeasureMesh
-
- Simple_MeasureShape - Class in mcib_plugins
-
*
/**
Copyright (C) 2008- 2012 Thomas Boudier and others
- Simple_MeasureShape() - Constructor for class mcib_plugins.Simple_MeasureShape
-
- Simple_MeasureStatistics - Class in mcib_plugins
-
*
/**
Copyright (C) 2008- 2012 Thomas Boudier and others
- Simple_MeasureStatistics() - Constructor for class mcib_plugins.Simple_MeasureStatistics
-
- simpleMeasure - Class in mcib_plugins.analysis
-
/**
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.
- simpleMeasure(ImagePlus) - Constructor for class mcib_plugins.analysis.simpleMeasure
-
- SingularValueDecomposition - Class in mcib3d.Jama
-
Singular Value Decomposition.
- SingularValueDecomposition(Matrix) - Constructor for class mcib3d.Jama.SingularValueDecomposition
-
Construct the singular value decomposition
- size() - Method in class mcib3d.Classification.Attributes
-
- size() - Method in class mcib3d.Classification.DataSet
-
- size() - Method in class mcib3d.image3d.regionGrowing.AssociationRegion
-
- size() - Method in class mcib3d.utils.ArrayUtil
-
- sizex - Variable in class mcib3d.align.Align2D
-
Description of the Field
- sizeX - Variable in class mcib3d.image3d.Coordinate3D
-
- sizeX - Variable in class mcib3d.image3d.ImageHandler
-
- sizex - Variable in class mcib3d.image3d.legacy.ColorImage3D
-
Deprecated.
Description of the Field
- sizex - Variable in class mcib3d.image3d.legacy.Image3D
-
Deprecated.
size x
- sizeXY - Variable in class mcib3d.image3d.Coordinate3D
-
- sizeXY - Variable in class mcib3d.image3d.ImageHandler
-
- sizeXYZ - Variable in class mcib3d.image3d.Coordinate3D
-
- sizeXYZ - Variable in class mcib3d.image3d.ImageHandler
-
- sizey - Variable in class mcib3d.align.Align2D
-
Description of the Field
- sizeY - Variable in class mcib3d.image3d.Coordinate3D
-
- sizeY - Variable in class mcib3d.image3d.ImageHandler
-
- sizey - Variable in class mcib3d.image3d.legacy.ColorImage3D
-
Deprecated.
Description of the Field
- sizey - Variable in class mcib3d.image3d.legacy.Image3D
-
Deprecated.
size y
- sizez - Variable in class mcib3d.align.Align2D
-
Description of the Field
- sizeZ - Variable in class mcib3d.image3d.Coordinate3D
-
- sizeZ - Variable in class mcib3d.image3d.ImageHandler
-
- sizez - Variable in class mcib3d.image3d.legacy.ColorImage3D
-
Deprecated.
Description of the Field
- sizez - Variable in class mcib3d.image3d.legacy.Image3D
-
Deprecated.
size z
- smooth(List, float) - Static method in class mcib3d.geom.MeshEditor
-
If the Content instance wraps a mesh, smooth it by the
fraction K (0, 1).
- smooth2(List<Point3f>, int) - Static method in class mcib3d.geom.MeshEditor
-
Implemented Blender-style vertex smoothing.
- SMOOTH_BLENDER - Static variable in class mcib3d.geom.Object3DSurface
-
- smooth_faces - Variable in class mcib3d.geom.Object3DSurface
-
- SMOOTH_IJ3D - Static variable in class mcib3d.geom.Object3DSurface
-
- SMOOTH_LAPLACE - Static variable in class mcib3d.geom.Object3DSurface
-
- sNew - Variable in class mcib3d.image3d.distanceMap3d.CleanUpLocalThickness
-
Deprecated.
- snr3D() - Method in class mcib3d.image3d.legacy.ColorImage3D
-
Deprecated.
Description of the Method
- snr3D() - Method in class mcib3d.image3d.legacy.IntImage3D
-
Deprecated.
Description of the Method
- SOBEL - Static variable in class mcib3d.image3d.processing.FastFilters3D
-
- sobelFilter() - Method in class mcib3d.image3d.ImageFloat
-
Sobel-like filtering in 3D
- sobelFilter() - Method in class mcib3d.image3d.ImageInt
-
Sobel-like filtering in 3D
- sobelFilter() - Method in class mcib3d.image3d.legacy.IntImage3D
-
Deprecated.
Sobel-like filtering in 3D
- solve(Matrix) - Method in class mcib3d.Jama.CholeskyDecomposition
-
Solve A*X = B
- solve(Matrix) - Method in class mcib3d.Jama.LUDecomposition
-
Solve A*X = B
- solve(Matrix) - Method in class mcib3d.Jama.Matrix
-
Solve A*X = B
- solve(Matrix) - Method in class mcib3d.Jama.QRDecomposition
-
Least squares solution of A*X = B
- solveTranspose(Matrix) - Method in class mcib3d.Jama.Matrix
-
Solve X*A = B, which is also A'*X' = B'
- sort(boolean, ImageHandler) - Method in class mcib3d.image3d.MaskIterator
-
Deprecated.
- sort() - Method in class mcib3d.utils.ArrayUtil
-
- sortIndexShellMeitzner() - Method in class mcib3d.utils.ArrayUtil
-
Get the indexes of sorted array (Shell-Meitzner algorithm) do not sort
the array
- sortJava() - Method in class mcib3d.utils.ArrayUtil
-
- sortMultithread() - Method in class mcib3d.utils.ArrayUtil
-
- sortPopulation() - Method in class mcib3d.geom.Objects3DPopulation
-
- sortShellMeitzner() - Method in class mcib3d.utils.ArrayUtil
-
Sort the array (Shell-Meitzner algorithm) increasing
- spatialAnalysis - Class in mcib_plugins.analysis
-
Description of the Class
- spatialAnalysis(int, int, double, double) - Constructor for class mcib_plugins.analysis.spatialAnalysis
-
- SpatialDescriptor - Interface in mcib3d.spatial.descriptors
-
- SpatialModel - Interface in mcib3d.spatial.sampler
-
- SpatialRandom - Class in mcib3d.spatial.sampler
-
- SpatialRandom(int, Object3D) - Constructor for class mcib3d.spatial.sampler.SpatialRandom
-
- SpatialRandomHardCore - Class in mcib3d.spatial.sampler
-
- SpatialRandomHardCore(int, double, Object3D) - Constructor for class mcib3d.spatial.sampler.SpatialRandomHardCore
-
- SpatialShuffle - Class in mcib3d.spatial.sampler
-
- SpatialShuffle(Objects3DPopulation) - Constructor for class mcib3d.spatial.sampler.SpatialShuffle
-
- SpatialStatistics - Class in mcib3d.spatial.analysis
-
- SpatialStatistics(SpatialDescriptor, SpatialModel, int, Objects3DPopulation) - Constructor for class mcib3d.spatial.analysis.SpatialStatistics
-
- split(int, int, int) - Method in class mcib3d.image3d.legacy.Image3D
-
Deprecated.
Split a image into sub images
- splitSpotProjection(IntImage3D, int, Object3D, int, int, double, float, int) - Static method in class mcib3d.image3d.Segment3DSpots
-
NOT USED, see splitSpotWatershed
- splitSpotWatershed(Object3D, float, float) - Static method in class mcib3d.image3d.Segment3DSpots
-
- Spot2D(int, ImageLabeller2D.Vox2D) - Constructor for class mcib3d.image3d.ImageLabeller2D.Spot2D
-
- Spot3D(int, ImageLabeller.Vox3D) - Constructor for class mcib3d.image3d.ImageLabeller.Spot3D
-
- stack - Variable in class mcib3d.geom.deformation3d.Deriche
-
- StackFolderOpener - Class in mcib3d.utils
-
Opens a folder of images as a stack.
- StackFolderOpener() - Constructor for class mcib3d.utils.StackFolderOpener
-
- start() - Method in class mcib3d.utils.Chrono
-
Description of the Method
- start - Variable in class mcib3d.utils.ThreadRunner
-
Start all given threads and wait on each of them until all are done.
- startAndJoin() - Method in class mcib3d.utils.ThreadRunner
-
- startAndJoin(Thread[]) - Static method in class mcib3d.utils.ThreadRunner
-
- startAndJoin(Thread[]) - Static method in class mcib3d.utils.ThreadUtil
-
Start all given threads and wait on each of them until all are done.
- STATE_DIE - Static variable in class mcib3d.image3d.IterativeThresholding.ObjectTrack
-
- STATE_DIVIDE - Static variable in class mcib3d.image3d.IterativeThresholding.ObjectTrack
-
- STATE_MOVE - Static variable in class mcib3d.image3d.IterativeThresholding.ObjectTrack
-
- STATE_UNKNOWN - Static variable in class mcib3d.image3d.IterativeThresholding.ObjectTrack
-
- Stats_Spat3D - Class in mcib_plugins
-
Description of the Class
- Stats_Spat3D() - Constructor for class mcib_plugins.Stats_Spat3D
-
- status - Variable in class mcib3d.image3d.IterativeThresholding.TrackThreshold
-
Deprecated.
- stDev - Variable in class mcib3d.image3d.legacy.Image3D
-
Deprecated.
std dev of the image
- stop() - Method in class mcib3d.utils.Chrono
-
Description of the Method
- substractImage(ImageHandler) - Method in class mcib3d.image3d.ImageHandler
-
Deprecated.
- substractImage(ImageInt) - Method in class mcib3d.image3d.ImageInt
-
Deprecated.
- substractMask(ImageInt) - Method in class mcib3d.image3d.ImageByte
-
- substractObject(Object3D) - Method in class mcib3d.geom.Object3DVoxels
-
- subtract(ImageFloat) - Method in class mcib3d.image3d.ImageFloat
-
- subtractImage(ImageHandler) - Method in class mcib3d.image3d.ImageHandler
-
- subtractImage(ImageInt) - Method in class mcib3d.image3d.ImageInt
-
- subtractImageInt(ImageInt) - Method in class mcib3d.image3d.ImageInt
-
- surfaceContact(Object3D, double) - Method in class mcib3d.geom.Object3D
-
Get the contact surfaces between two objects, outside voxels < dist and
number of border voxels of this object included in the objectB
- surrounds() - Method in class mcib3d.geom.MereoObject3D
-
- svd() - Method in class mcib3d.Jama.Matrix
-
Singular Value Decomposition
- swapQuadrants() - Method in class mcib3d.image3d.legacy.FHTImage3D
-
Deprecated.
Description of the Method
- SymmetryFilter - Class in mcib3d.image3d.processing
-
From the article Gertych et al., Computers in Biology and Medicine 2015
- SymmetryFilter(ImageHandler[], int, boolean) - Constructor for class mcib3d.image3d.processing.SymmetryFilter
-