Object3D

java.lang.Object
- mcib3d.geom.Object3D

All Implemented Interfaces:

java.lang.Comparable<Object3D>

Direct Known Subclasses:

Object3DLabel, Object3DSurface, Object3DVoxels
```
public abstract class Object3D
extends java.lang.Object
implements java.lang.Comparable<Object3D>
```
Copyright (C) 2008- 2011 Thomas Boudier

This file is part of mcib3d
mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see .
package mcib3d.geom;
/** Abstract class for 3D objects, compute various measurements, and also distance analysis.

Field Summary

Fields
Modifier and Type	Field and Description
`protected double`	`areaContactUnit` Area in units
`protected double`	`areaContactVoxels`
`protected double`	`areaNbVoxels` Area in voxels
`protected double`	`bx` IsoBarycenter x
`protected double`	`by` IsoBarycenter x
`protected double`	`bz` IsoBarycenter y
`protected java.lang.String`	`comment` comment on the object (not used yet)
`double`	`compare`
`protected java.util.LinkedList<Voxel3D>`	`contours` Contours pixels
`protected ImageHandler`	`currentQuantifImage` current image used for quantification (to compute results once)
`protected double`	`cx` Center of mass x
`protected double`	`cy` Center of mass y
`protected double`	`cz` Center of mass z
`protected EigenvalueDecomposition`	`eigen` Matrix of decomposition
`protected double`	`feret` feret diameter
`protected Voxel3D`	`feret1` Pixel 1 for feret diameter
`protected Voxel3D`	`feret2` Pixel 2 for feret diameter
`protected double`	`integratedDensity` Integrated density (sum of pixels)
`protected KDTreeC`	`kdtreeContours` kd-tree for the contour
`protected ImageHandler`	`labelImage` label image, starts at 0,0,0
`protected double`	`meanDensity`
`static byte`	`MEASURE_AREA_PIX`
`static byte`	`MEASURE_AREA_UNIT`
`static byte`	`MEASURE_COMPACTNESS_UNITS`
`static byte`	`MEASURE_COMPACTNESS_VOXELS`
`static byte`	`MEASURE_DC_AVG`
`static byte`	`MEASURE_DC_SD`
`static byte`	`MEASURE_INTENSITY_AVG`
`static byte`	`MEASURE_INTENSITY_MAX`
`static byte`	`MEASURE_INTENSITY_MEDIAN`
`static byte`	`MEASURE_INTENSITY_MIN`
`static byte`	`MEASURE_INTENSITY_SD`
`static byte`	`MEASURE_MAIN_ELONGATION`
`static byte`	`MEASURE_NONE`
`static byte`	`MEASURE_VOLUME_PIX`
`static byte`	`MEASURE_VOLUME_UNIT`
`protected ImageInt`	`miniLabelImage` The image where the object lies with offset usually xmin, ymin and zmin
`boolean`	`multiThread` use multithreading mode (not used ?)
`protected java.lang.String`	`name` name the object (not used yet)
`protected double`	`pixmax` Max pix value in object
`protected double`	`pixmin` Min pix value in object
`protected double`	`resXY` the resolution in XY
`protected double`	`resZ` the resolution in Z
`protected double`	`s002`
`protected double`	`s003`
`protected double`	`s004`
`protected double`	`s011`
`protected double`	`s012`
`protected double`	`s013`
`protected double`	`s020`
`protected double`	`s021`
`protected double`	`s022`
`protected double`	`s030`
`protected double`	`s031`
`protected double`	`s040`
`protected double`	`s101`
`protected double`	`s102`
`protected double`	`s103`
`protected double`	`s110`
`protected double`	`s111`
`protected double`	`s112`
`protected double`	`s120`
`protected double`	`s121`
`protected double`	`s130`
`double`	`s200` Centred Moments order 2
`protected double`	`s201`
`protected double`	`s202`
`protected double`	`s210`
`protected double`	`s211`
`protected double`	`s220`
`protected double`	`s300` Centred Moments order 3
`protected double`	`s301`
`protected double`	`s310`
`protected double`	`s400` Centred Moments order 4
`protected double`	`sigma` standard deviation
`protected int`	`type` category of the object (not used yet)
`protected java.lang.String`	`units` the unit for resolution
`protected int`	`value` Value (grey-level)
`boolean`	`verbose` use verbose mode (not used ?)
`protected int`	`volume` volume in voxels
`protected int`	`xmax` Bounding box
`protected int`	`xmin` Bounding box
`protected int`	`ymax` Bounding box
`protected int`	`ymin` Bounding box
`protected int`	`zmax` Bounding box
`protected int`	`zmin` Bounding box

Constructor Summary

Constructors
Constructor and Description

Object3D()

Constructors
Constructor and Description
`Object3D()`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`double`	`angle(Object3D a, Object3D b)` Angle between (a, this, b) with real coordinates
`boolean`	`b_closed(float radX, float radY, float radZ)`
`boolean`	`b_open(float radX, float radY, float radZ)`
`boolean`	`centerInside()`
`int`	`compareTo(Object3D o)`
`protected abstract void`	`computeBounding()` Compute the bounding box of the object
`protected abstract void`	`computeCenter()` Compute the barycenter of the object
`abstract void`	`computeContours()` Compute the contour voxels of the object
`void`	`computeContours(ImageHandler ima)` The contours is given in an image (see OC3D)
`protected void`	`computeEigen()` Constructor for the computeEigen object
`protected abstract void`	`computeMassCenter(ImageHandler ima)` Compute the mass center of the object using signal from an image
`protected abstract void`	`computeMassCenter(ImageHandler ima, ImageHandler mask)` Compute the mass center of the object using signal from an image and within a mask
`java.util.List`	`computeMeshSurface(boolean calibrated)` Deprecated. use Object3D-IJUtils
`protected abstract void`	`computeMoments2(boolean normalize)` Compute the moments of the object (for ellipsoid orientation), order 2
`protected abstract void`	`computeMoments3()` Compute the moments of the object, order 3
`protected abstract void`	`computeMoments4()` Compute the moments of the object, order 4
`ImageHandler`	`createIntersectionImage(Object3D other, int val1, int val2)` Create an intersection image around two objects (with no extra borders)
`ImageHandler`	`createIntersectionImage(Object3D other, int val1, int val2, int border)` Create an intersection image around two objects
`abstract Roi`	`createRoi(int z)` Deprecated. use Object3D-IJUtils create a roi for a slice
`ImageHandler`	`createSegImage(int bx, int by, int bz)`
`ImageHandler`	`createSegImage(int xmi, int ymi, int zmi, int xma, int yma, int zma, int val)`
`ImageInt`	`createSegImageMini2D(int val, int borderSize)`
`boolean`	`disjointBox(Object3D other)`
`double`	`distBorderPixel(Object3D other)` the minimum distance between two objets (in real distance) computed on the contours pixels
`double`	`distBorderUnit(Object3D other)` the minimum distance between two objets (in real distance) computed on the contours pixels
`double`	`distBorderUnit(Point3D point0, Object3D other, Point3D point1, boolean opposite)` The border to border distance along a direction (EXPERIMENTAL)
`double`	`distCenter2DUnit(Object3D autre)` 2D distance from center to center (in real distance)
`double`	`distCenterBorderUnit(Object3D autre)` Distance center of this object to the border of the other
`double`	`distCenterPixel(Object3D other)` distance from center to center (in pixel)
`double`	`distCenterUnit(Object3D autre)` distance from center to center (in real distance)
`double`	`distHausdorffUnit(Object3D other)`
`double`	`distPixelBorder(Point3D P)`
`double`	`distPixelBorderUnit(double x, double y, double z)` Distance from a point to the border of the object
`double`	`distPixelBorderUnit(double x, double y, double z, Vector3D V)` Distance from a point along a direction to the border of the object
`double`	`distPixelCenter(double x, double y, double z)` The distance between center and a point with coordinates
`double`	`distPixelCenter(Point3D P)` The distance between center and a Point3D
`abstract boolean`	`draw(ByteProcessor mask, int z, int col)` Deprecated. use Object3D-IJUtils drawing inside a 2D byteprocessor
`void`	`draw(ImageHandler mask)` Drawing inside an image, with default value = object value
`abstract void`	`draw(ImageHandler mask, float val)` drawing inside an ImageHandler
`abstract void`	`draw(ImageHandler mask, int col, int tx, int ty, int tz)`
`abstract void`	`draw(ImageStack mask, int col)` Deprecated. use Object3D-IJUtils drawing inside an imagestack
`abstract void`	`draw(ImageStack mask, int r, int g, int b)` Deprecated. use Object3D-IJUtils drawing inside an imagestack, in rgb color
`abstract void`	`draw(ObjectCreator3D obj, int col)` drawing inside an objectCreator
`void`	`drawAt(ImageHandler mask, int col, Point3D center)`
`void`	`drawLink(ImageHandler mask, Object3D other, int col)` Drawing links between two objects
`int`	`edgeContact(Object3D other, int distSquareMax)`
`boolean`	`edgeImage(ImageHandler img, boolean edgeXY, boolean edgeZ)`
`double`	`getAreaPixels()` the area of the Object3D (in pixels)
`double`	`getAreaUnit()` Gets the areaUnit attribute of the Object3D object
`float[]`	`getArrayValues(ImageHandler ima)` Gets the list of values inside an image as an array
`int[]`	`getBoundingBox()` Get the bounding box of the object (Xmin, Xmax, Ymin, Ymax, Zmin, Zmax)
`java.util.ArrayList<Voxel3D>`	`getBoundingOriented()`
`Calibration`	`getCalibration()` Deprecated. use Object3D-IJUtils Gets the calibration of the Object3D (ImageJ)
`double[]`	`getCenterAsArray()`
`Point3D`	`getCenterAsPoint()` Gets the center attribute of the Object3D object
`Vector3D`	`getCenterAsVector()` Gets the center attribute of the Object3D object
`Vector3D`	`getCenterAsVectorUnit()` Gets the center attribute of the Object3D object
`Vector3D`	`getCenterUnit()` Gets the centerUnit attribute of the Object3D object
`double`	`getCenterX()` x coordinate of the center
`double`	`getCenterY()` y coordinate of the center
`double`	`getCenterZ()` z coordinate of the center
`Object3DVoxels`	`getClosedObject(float radX, float radY, float radZ)`
`abstract int`	`getColoc(Object3D obj)`
`java.lang.String`	`getComment()`
`double`	`getCompactness()`
`double`	`getCompactness(boolean useUnit)` Gets the compactness attribute of the Object3D (unit) related to sphericity
`java.util.LinkedList<Voxel3D>`	`getContours()` return the list of contour voxels
`Object3DVoxels`	`getConvexObject()`
`Object3DVoxels`	`getConvexObject(boolean multi)`
`PolygonRoi`	`getConvexPolygonRoi(int z)`
`Object3DSurface`	`getConvexSurface()`
`Object3DVoxels`	`getDilatedObject(float radX, float radY, float radZ)`
`double`	`getDistCenterMax()` the maximum distance between center and contours
`double`	`getDistCenterMaxPixel()` the maximum distance between center and contours
`double`	`getDistCenterMean()` the average distance between center and contours
`double`	`getDistCenterMeanPixel()` the average distance between center and contours
`double`	`getDistCenterMin()` the minimum distance between center and contours
`double`	`getDistCenterMinPixel()` the minimum distance between center and contours
`double`	`getDistCenterSigma()` the sigma value for distances between center and contours
`double`	`getDistCenterSigmaPixel()` the sigma value for distances between center and contours
`Object3DVoxels`	`getEllipsoid()`
`Object3DVoxels`	`getErodedObject(float radX, float radY, float radZ)`
`double`	`getFeret()` Gets the feret diameter of the object (unit)
`Voxel3D`	`getFeretVoxel1()` Gets the first feret voxel of the object (unit)
`Voxel3D`	`getFeretVoxel2()` Gets the second feret voxel of the object (unit)
`double[]`	`getGeometricInvariants()` Compute geometric invariants, based on orders 4 moments refer to Xu and Li 2008.
`double[]`	`getHomogeneousInvariants()` Compute homogeneous invariants, based on orders 4 moments
`double`	`getIntegratedDensity(ImageHandler ima)` integrated density of the Object3D in an image
`double`	`getIntegratedDensity(ImageHandler ima, ImageHandler mask)`
`protected int[]`	`getIntersectionBox(Object3D other)`
`Object3DVoxels`	`getIntersectionObject(Object3D other)` Get the intersection voxels as a 3D object
`ImageHandler`	`getLabelImage()` Gets the label image of the object (should start at 0,0
`Object3DVoxels`	`getLayerEVFObject(ImageInt mask, float ratio)`
`Object3DVoxels`	`getLayerEVFObject(Object3D mask, float ratio)`
`Object3DVoxels`	`getLayerObject(float r1, float r2)`
`Vector3D`	`getMainAxis()` Gets the mainAxis attribute of the Object3D object (unit)
`double`	`getMainElongation()` Gets the main elongation of the object
`double`	`getMassCenterX(ImageHandler ima)` x coordinate of the center of mass in an image
`double`	`getMassCenterY(ImageHandler ima)` u coordinate of the center of mass in an image
`double`	`getMassCenterZ(ImageHandler ima)` z coordinate of the center of mass in an image
`Matrix`	`getMatrixAxes()` Gets the main axes vectors as a matrix
`ImageHandler`	`getMaxLabelImage(int val)` Get the label image starting at 0,0,0
`double`	`getMeanPixValueAroundBarycenter(boolean massCenter, ImageInt objectMap, ImageHandler ima, double radXY, double radZ)`
`double`	`getMeasure(int Measure)` Utility to perform measurement
`double`	`getMedianElongation()` Gets the flatness of the object
`double[]`	`getMoments3D()` This code is taken from the BIOCAT platform: http://faculty.cs.niu.edu/~zhou/tool/biocat/ Reference for BIOCAT: J.
`double[]`	`getMomentsRaw2()` Returns the moments order 2
`double[]`	`getMomentsRaw3()` Returns the moments order 3
`double[]`	`getMomentsRaw4()` Returns the moments order 4
`java.lang.String`	`getName()` The name of the object
`static int`	`getNbMoments3D()`
`int[]`	`getNumbering(ImageHandler ima)` Will count the number of different objects within this object *
`Object3DSurface`	`getObject3DSurface()` Convert the object to surface (if necessary)
`Object3DVoxels`	`getObject3DVoxels()` Convert the object to voxels (if necessary)
`Object3DVoxels`	`getOpenedObject(float radX, float radY, float radZ)`
`double`	`getPixCenterValue(ImageHandler ima)`
`Voxel3D`	`getPixelBorder(double x, double y, double z)`
`abstract Voxel3D`	`getPixelMax(ImageHandler ima)` compute the voxel with maximum value in an image
`double`	`getPixMaxValue(ImageHandler ima)` Gets the pixMaxValue attribute of the Object3D object
`double`	`getPixMeanValue(ImageHandler ima)` Gets the meanPixValue attribute of the Object3D object
`double`	`getPixMeanValueContour(ImageHandler ima)`
`double`	`getPixMedianValue(ImageHandler ima)`
`double`	`getPixMinValue(ImageHandler ima)` Gets the pixMinValue attribute of the Object3D object
`double`	`getPixModeNonZero(ImageHandler ima)`
`double`	`getPixModeValue(ImageHandler ima)`
`double`	`getPixStdDevValue(ImageHandler ima)` Gets the SD of pixels in object
`double`	`getQuantilePixValue(ImageHandler ima, double quantile)` Gets the quantile value of the object in the image
`double`	`getRadiusMoments(int order)`
`double`	`getRatioBox()` Gets the ration between volume and volume of the bounding box (in units)
`double`	`getRatioEllipsoid()` Gets the ration between volume and volume of the ellipsoid (in units)
`double`	`getResXY()` Gets the calibration in XY of the Object3D
`double`	`getResZ()` Gets the calibration in Z of the Object3D
`double`	`getSphericity()`
`double`	`getSphericity(boolean useUnit)` Gets the sphericity attribute of the Object3D (unit) related to compactness
`int`	`getType()` The type
`java.lang.String`	`getUnits()` Gets the unit attribute of the Object3D object
`int`	`getValue()` Value of the Object3D
`double`	`getValueAxis(int order)` Gets the valueAxis attribute of the Object3D object (unit)
`Vector3D`	`getVectorAxis(int order)` Gets the Axis attribute of the Object3D object (unit)
`double`	`getVolumeBoundingBoxOrientedPixel()` the volume of the oriented bounding box FIXME computing of oriented box
`double`	`getVolumeBoundingBoxPixel()` the volume of the bounding box
`double`	`getVolumeEllipseUnit()` The volume of the approximated ellipsoid in unit the main radius is DCMax
`int`	`getVolumePixels()` volume of the Object3D (in pixel)
`double`	`getVolumeUnit()` Gets the volume of the Object3D in units
`abstract java.util.List<Voxel3D>`	`getVoxels()` Get the list of voxels of the object
`int`	`getXmax()` Gets the xmax attribute of the Object3D
`int`	`getXmin()` Gets the xmin attribute of the Object3D
`int`	`getYmax()` Gets the ymax attribute of the Object3D
`int`	`getYmin()` Gets the ymin attribute of the Object3D
`int`	`getZmax()` Gets the zmax attribute of the Object3D
`int`	`getZmin()` Gets the zmin attribute of the Object3D
`abstract boolean`	`hasOneVoxelColoc(Object3D obj)`
`abstract boolean`	`hasOneVoxelValueRange(ImageHandler img, int t0, int t1)`
`boolean`	`includedInZonesNone(ImageInt imageZones)`
`boolean`	`includedInZonesOneMore(ImageInt imageZones)`
`boolean`	`includedInZonesOneOnly(ImageInt imageZones)`
`boolean`	`includes(Object3D obj)`
`boolean`	`includesBox(Object3D autre)` Test if the bouding boxes intersect
`boolean`	`includesMarkersNone(ImageInt imageMarkers)`
`boolean`	`includesMarkersOneMore(ImageInt imageMarkers)`
`boolean`	`includesMarkersOneOnly(ImageInt imageMarkers)`
`void`	`init()` Init default values and compute contours and center
`boolean`	`inside(double x, double y, double z)` test if the point is inside the object
`boolean`	`inside(Point3D P)`
`boolean`	`insideAll(java.util.ArrayList<Point3D> markers)`
`boolean`	`insideBounding(double x, double y, double z)` test if the point is inside the bounding box of the object
`boolean`	`insideBounding(double x, double y, double z, int rx, int ry, int rz)`
`boolean`	`insideBounding(float x, float y, float z)` test if the point is inside the bounding box of the object
`boolean`	`insideOne(java.util.ArrayList<Point3D> markers)`
`boolean`	`isContour(Voxel3D vox)`
`boolean`	`isEmpty()`
`abstract ArrayUtil`	`listValues(ImageHandler ima)` Outputs the list of Voxels values using intensity image
`abstract ArrayUtil`	`listValues(ImageHandler ima, float thresh)` Outputs the list of Voxels values using intensity image above a fixed threshold
`java.util.List<Voxel3D>`	`listVoxels(ImageHandler ima)` gets the list of all pixels within an image as an ArrayList
`abstract java.util.List<Voxel3D>`	`listVoxels(ImageHandler ima, double thresh)` List Voxels in the image with values > threshold
`abstract java.util.List<Voxel3D>`	`listVoxels(ImageHandler ima, double thresh0, double thres1)` List Voxels in the image with values > threshold0 and < threshold1
`java.util.List<Voxel3D>`	`listVoxelsByDistance(Point3D P0, double dist0, double dist1, boolean contourOnly)` List Voxels in the image with with distances in specific range from a reference point
`protected java.lang.String`	`loadInfo(java.io.BufferedReader bf)`
`boolean`	`overlapBox(Object3D other)`
`double`	`pcColoc(Object3D obj)` Percentage of colocalisation between two objects relative to this object
`static double`	`pcColocSum(Object3D A, Object3D B)`
`Point3D`	`pointPixelBorder(double x, double y, double z, Vector3D V)` Vector from a point along a direction to the border of the object
`double`	`radiusCenter(Object3D obj)` the radius of the object towards another object
`double`	`radiusCenter(Object3D obj, boolean opposite)` the radius of the object towards another object, in forward or opposite direction
`double`	`radiusCenter(Vector3D V)` the radius along a direction
`double`	`radiusPixel(double x, double y, double z)` the radius towards a point
`boolean`	`regular(float radX, float radY, float radZ)`
`void`	`resetQuantifImage()`
`protected void`	`saveInfo(java.io.BufferedWriter bf)`
`abstract void`	`saveObject(java.lang.String path)`
`void`	`setCalibration(Calibration cal)` Deprecated. use Object3D-IJUtils Sets the calibration of the Object3D (ImageJ)
`void`	`setCalibration(double rxy, double rz, java.lang.String u)` Sets the calibration of the Object3D
`void`	`setComment(java.lang.String comment)`
`void`	`setLabelImage(ImageInt labelImage)` Sets the label image of the object (should start at 0,0,0)
`void`	`setName(java.lang.String name)` Sets the name
`void`	`setNewCenter(double x, double y, double z)`
`void`	`setNewCenter(Object3D obj)`
`void`	`setNewCenter(Vector3D newCenter)`
`void`	`setResXY(double rxy)` Sets the calibration in XY of the Object3D
`void`	`setResZ(double rz)` Sets the calibration in Z of the Object3D
`void`	`setType(int type)` Sets the type
`void`	`setUnits(java.lang.String u)` Sets the units attribute for the calibration
`void`	`setValue(int v)` Sets the value attribute of the Object3D object
`int[]`	`surfaceContact(Object3D other, double dist_max)` Get the contact surfaces between two objects, outside voxels < dist and number of border voxels of this object included in the objectB
`java.lang.String`	`toString()` Display information
`boolean`	`touchBorders(ImageHandler img, boolean Z)`
`boolean`	`touchBorders(ImagePlus img, boolean Z)` Deprecated. use Object3D-IJUtils
`abstract void`	`translate(double x, double y, double z)`
`void`	`translate(Vector3D V)`
`Vector3D`	`vectorBorderBorder(Object3D other)` Gets the areaUnit attribute of the Object3D object
`Vector3D`	`vectorBorderBorder(Point3D point0, Object3D other, Point3D point1, boolean opposite)` The vector between V0 and V1 : V0 is the point on border of object from point0 along direction V1 is the point on border of other object from point1 along opposite direction
`Vector3D`	`vectorCenterBorder(Object3D other)` The vector between the center of this object and the border of the other object
`Vector3D`	`vectorPixelBorder(double x, double y, double z)` Vector between a pixel and the closest border
`Vector3D`	`vectorPixelBorder(double x, double y, double z, Vector3D V)` Vector from a point along a direction to the border of the object The distance is the distance to the point where there is a change in the object appartenance (inside / outside)
`Vector3D`	`vectorPixelBorder(Vector3D V)` Vector between a voxel defined by a vector and the closest border
`Vector3D`	`vectorPixelUnitBorder(double x, double y, double z)` vector between a pixel and the border the point is given is real units
`Vector3D`	`vectorPixelUnitBorder(double x, double y, double z, Vector3D dir)` vector between a pixel and the border, along a direction the vector is given is real units
`Vector3D`	`vectorPixelUnitBorder(Vector3D V)` vector between a point and the border the vector is given is real units
`Vector3D`	`vectorPixelUnitBorder(Vector3D V, Vector3D dir)` vector between a point and the border along a direction the point is given is real units
`Voxel3D[]`	`VoxelsBorderBorder(Object3D other)` Return the two voxels defining the border-border distance

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - MEASURE_NONE
```
public static final byte MEASURE_NONE
```
    See Also:
    
    Constant Field Values
  - MEASURE_VOLUME_PIX
```
public static final byte MEASURE_VOLUME_PIX
```
    See Also:
    
    Constant Field Values
  - MEASURE_VOLUME_UNIT
```
public static final byte MEASURE_VOLUME_UNIT
```
    See Also:
    
    Constant Field Values
  - MEASURE_MAIN_ELONGATION
```
public static final byte MEASURE_MAIN_ELONGATION
```
    See Also:
    
    Constant Field Values
  - MEASURE_COMPACTNESS_VOXELS
```
public static final byte MEASURE_COMPACTNESS_VOXELS
```
    See Also:
    
    Constant Field Values
  - MEASURE_COMPACTNESS_UNITS
```
public static final byte MEASURE_COMPACTNESS_UNITS
```
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    Constant Field Values
  - MEASURE_AREA_PIX
```
public static final byte MEASURE_AREA_PIX
```
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    Constant Field Values
  - MEASURE_AREA_UNIT
```
public static final byte MEASURE_AREA_UNIT
```
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    Constant Field Values
  - MEASURE_DC_AVG
```
public static final byte MEASURE_DC_AVG
```
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    Constant Field Values
  - MEASURE_DC_SD
```
public static final byte MEASURE_DC_SD
```
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    Constant Field Values
  - MEASURE_INTENSITY_AVG
```
public static final byte MEASURE_INTENSITY_AVG
```
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    Constant Field Values
  - MEASURE_INTENSITY_SD
```
public static final byte MEASURE_INTENSITY_SD
```
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    Constant Field Values
  - MEASURE_INTENSITY_MIN
```
public static final byte MEASURE_INTENSITY_MIN
```
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    Constant Field Values
  - MEASURE_INTENSITY_MAX
```
public static final byte MEASURE_INTENSITY_MAX
```
    See Also:
    
    Constant Field Values
  - MEASURE_INTENSITY_MEDIAN
```
public static final byte MEASURE_INTENSITY_MEDIAN
```
    See Also:
    
    Constant Field Values
  - s200
```
public double s200
```
    Centred Moments order 2
  - verbose
```
public boolean verbose
```
    use verbose mode (not used ?)
  - multiThread
```
public boolean multiThread
```
    use multithreading mode (not used ?)
  - compare
```
public double compare
```
  - name
```
protected java.lang.String name
```
    name the object (not used yet)
  - type
```
protected int type
```
    category of the object (not used yet)
  - comment
```
protected java.lang.String comment
```
    comment on the object (not used yet)
  - xmin
```
protected int xmin
```
    Bounding box
  - ymin
```
protected int ymin
```
    Bounding box
  - zmin
```
protected int zmin
```
    Bounding box
  - xmax
```
protected int xmax
```
    Bounding box
  - ymax
```
protected int ymax
```
    Bounding box
  - zmax
```
protected int zmax
```
    Bounding box
  - bx
```
protected double bx
```
    IsoBarycenter x
  - by
```
protected double by
```
    IsoBarycenter x
  - bz
```
protected double bz
```
    IsoBarycenter y
  - cx
```
protected double cx
```
    Center of mass x
  - cy
```
protected double cy
```
    Center of mass y
  - cz
```
protected double cz
```
    Center of mass z
  - areaNbVoxels
```
protected double areaNbVoxels
```
    Area in voxels
  - areaContactUnit
```
protected double areaContactUnit
```
    Area in units
  - areaContactVoxels
```
protected double areaContactVoxels
```
  - volume
```
protected int volume
```
    volume in voxels
  - feret
```
protected double feret
```
    feret diameter
  - feret1
```
protected Voxel3D feret1
```
    Pixel 1 for feret diameter
  - feret2
```
protected Voxel3D feret2
```
    Pixel 2 for feret diameter
  - integratedDensity
```
protected double integratedDensity
```
    Integrated density (sum of pixels)
  - meanDensity
```
protected double meanDensity
```
  - sigma
```
protected double sigma
```
    standard deviation
  - pixmin
```
protected double pixmin
```
    Min pix value in object
  - pixmax
```
protected double pixmax
```
    Max pix value in object
  - value
```
protected int value
```
    Value (grey-level)
  - contours
```
protected java.util.LinkedList<Voxel3D> contours
```
    Contours pixels
  - kdtreeContours
```
protected KDTreeC kdtreeContours
```
    kd-tree for the contour
  - s110
```
protected double s110
```
  - s101
```
protected double s101
```
  - s020
```
protected double s020
```
  - s011
```
protected double s011
```
  - s002
```
protected double s002
```
  - s300
```
protected double s300
```
    Centred Moments order 3
  - s210
```
protected double s210
```
  - s201
```
protected double s201
```
  - s030
```
protected double s030
```
  - s120
```
protected double s120
```
  - s021
```
protected double s021
```
  - s003
```
protected double s003
```
  - s102
```
protected double s102
```
  - s012
```
protected double s012
```
  - s111
```
protected double s111
```
  - s400
```
protected double s400
```
    Centred Moments order 4
  - s040
```
protected double s040
```
  - s004
```
protected double s004
```
  - s220
```
protected double s220
```
  - s202
```
protected double s202
```
  - s022
```
protected double s022
```
  - s121
```
protected double s121
```
  - s112
```
protected double s112
```
  - s211
```
protected double s211
```
  - s103
```
protected double s103
```
  - s301
```
protected double s301
```
  - s130
```
protected double s130
```
  - s310
```
protected double s310
```
  - s013
```
protected double s013
```
  - s031
```
protected double s031
```
  - eigen
```
protected EigenvalueDecomposition eigen
```
    Matrix of decomposition
  - miniLabelImage
```
protected ImageInt miniLabelImage
```
    The image where the object lies with offset usually xmin, ymin and zmin
  - labelImage
```
protected ImageHandler labelImage
```
    label image, starts at 0,0,0
  - currentQuantifImage
```
protected ImageHandler currentQuantifImage
```
    current image used for quantification (to compute results once)
  - resXY
```
protected double resXY
```
    the resolution in XY
  - resZ
```
protected double resZ
```
    the resolution in Z
  - units
```
protected java.lang.String units
```
    the unit for resolution
- Constructor Detail
  - Object3D
```
public Object3D()
```
- Method Detail
  - getNbMoments3D
```
public static int getNbMoments3D()
```
  - pcColocSum
```
public static double pcColocSum(Object3D A,
                                Object3D B)
```
    Parameters:
    
    A -
    
    B -
    
    Returns:
  - getResXY
```
public double getResXY()
```
    Gets the calibration in XY of the Object3D
    
    Returns:
    
    The resXY value
  - setResXY
```
public void setResXY(double rxy)
```
    Sets the calibration in XY of the Object3D
    
    Parameters:
    
    rxy - The new calibration in XY
  - getResZ
```
public double getResZ()
```
    Gets the calibration in Z of the Object3D
    
    Returns:
    
    The resZ value
  - setResZ
```
public void setResZ(double rz)
```
    Sets the calibration in Z of the Object3D
    
    Parameters:
    
    rz - he new calibration in Z
  - getUnits
```
public java.lang.String getUnits()
```
    Gets the unit attribute of the Object3D object
    
    Returns:
    
    The units
  - setUnits
```
public void setUnits(java.lang.String u)
```
    Sets the units attribute for the calibration
    
    Parameters:
    
    u - The new units value
  - getCalibration
```
public Calibration getCalibration()
```
    Deprecated. use Object3D-IJUtils Gets the calibration of the Object3D (ImageJ)
    
    Returns:
    
    The calibration
  - setCalibration
```
public void setCalibration(Calibration cal)
```
    Deprecated. use Object3D-IJUtils Sets the calibration of the Object3D (ImageJ)
    
    Parameters:
    
    cal - The new calibration
  - setCalibration
```
public final void setCalibration(double rxy,
                                 double rz,
                                 java.lang.String u)
```
    Sets the calibration of the Object3D
    
    Parameters:
    
    rxy - The new calibration in XY
    
    rz - The new calibration in Z
    
    u - The new calibration units
  - getName
```
public java.lang.String getName()
```
    The name of the object
    
    Returns:
    
    name
  - setName
```
public void setName(java.lang.String name)
```
    Sets the name
    
    Parameters:
    
    name -
  - getType
```
public int getType()
```
    The type
    
    Returns:
    
    type
  - setType
```
public void setType(int type)
```
    Sets the type
    
    Parameters:
    
    type -
  - getComment
```
public java.lang.String getComment()
```
  - setComment
```
public void setComment(java.lang.String comment)
```
  - getLabelImage
```
public ImageHandler getLabelImage()
```
    Gets the label image of the object (should start at 0,0
    
    Returns:
    
    the image with the labelled object
  - setLabelImage
```
public void setLabelImage(ImageInt labelImage)
```
    Sets the label image of the object (should start at 0,0,0)
    
    Parameters:
    
    labelImage -
  - getMaxLabelImage
```
public ImageHandler getMaxLabelImage(int val)
```
    Get the label image starting at 0,0,0
    
    Parameters:
    
    val - the value to draw the binary mask
    
    Returns:
    
    The binary mask for the object
  - getVolumePixels
```
public int getVolumePixels()
```
    volume of the Object3D (in pixel)
    
    Returns:
    
    the volume
  - getMeasure
```
public double getMeasure(int Measure)
```
    Utility to perform measurement
    
    Parameters:
    
    Measure - The index of the measurement
    
    Returns:
    
    the measurement
  - getVolumeUnit
```
public double getVolumeUnit()
```
    Gets the volume of the Object3D in units
    
    Returns:
    
    The calibrated volume
  - computeCenter
```
protected abstract void computeCenter()
```
    Compute the barycenter of the object
  - computeMassCenter
```
protected abstract void computeMassCenter(ImageHandler ima)
```
    Compute the mass center of the object using signal from an image
    
    Parameters:
    
    ima - the image with the signal intensity
  - computeMassCenter
```
protected abstract void computeMassCenter(ImageHandler ima,
                                          ImageHandler mask)
```
    Compute the mass center of the object using signal from an image and within a mask
    
    Parameters:
    
    ima - the image with the signal intensity
    
    mask - the mask to restrain the computation
  - getArrayValues
```
public float[] getArrayValues(ImageHandler ima)
```
    Gets the list of values inside an image as an array
    
    Parameters:
    
    ima - image
    
    Returns:
    
    the array of pixel values
  - getQuantilePixValue
```
public double getQuantilePixValue(ImageHandler ima,
                                  double quantile)
```
    Gets the quantile value of the object in the image
    
    Parameters:
    
    ima - image
    
    Returns:
    
    the quantile value
  - computeBounding
```
protected abstract void computeBounding()
```
    Compute the bounding box of the object
  - computeContours
```
public abstract void computeContours()
```
    Compute the contour voxels of the object
  - computeMoments2
```
protected abstract void computeMoments2(boolean normalize)
```
    Compute the moments of the object (for ellipsoid orientation), order 2
    
    Parameters:
    
    normalize - normalize by volume or not
  - computeMoments3
```
protected abstract void computeMoments3()
```
    Compute the moments of the object, order 3
  - computeMoments4
```
protected abstract void computeMoments4()
```
    Compute the moments of the object, order 4
  - getMomentsRaw2
```
public double[] getMomentsRaw2()
```
    Returns the moments order 2
    
    Returns:
    
    the moments (6)
  - getMomentsRaw3
```
public double[] getMomentsRaw3()
```
    Returns the moments order 3
    
    Returns:
    
    the moments (10)
  - getMomentsRaw4
```
public double[] getMomentsRaw4()
```
    Returns the moments order 4
    
    Returns:
    
    the moments (15)
  - getGeometricInvariants
```
public double[] getGeometricInvariants()
```
    Compute geometric invariants, based on orders 4 moments refer to Xu and Li 2008. Geometric moments invariants. Pattern recognition. doi:10.1016/j.patcog.2007.05.001
    
    Returns:
    
    the invariants (6)
  - getHomogeneousInvariants
```
public double[] getHomogeneousInvariants()
```
    Compute homogeneous invariants, based on orders 4 moments
    
    Returns:
    
    the invariants (5)
  - getMoments3D
```
public double[] getMoments3D()
```
    This code is taken from the BIOCAT platform: http://faculty.cs.niu.edu/~zhou/tool/biocat/ Reference for BIOCAT: J. Zhou, S. Lamichhane, G. Sterne, B. Ye, H. C. Peng, "BIOCAT: a Pattern Recognition Platform for Customizable Biological Image Classification and Annotation", BMC Bioinformatics , 2013, 14:291 * This class calculates a set of five 3D image moments that are invariant to size, position and orientation. Reference: F. A. Sadjadi and E. L. Hall, Three-Dimensional Moment Invariants, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. PAMI-2, no. 2, pp. 127-136, March 1980.
    
    Returns:
    
    3D moments (5)
  - getPixelMax
```
public abstract Voxel3D getPixelMax(ImageHandler ima)
```
    compute the voxel with maximum value in an image
    
    Parameters:
    
    ima - the image
    
    Returns:
    
    the max voxel
  - listVoxels
```
public java.util.List<Voxel3D> listVoxels(ImageHandler ima)
```
    gets the list of all pixels within an image as an ArrayList
    
    Parameters:
    
    ima - the image with signal
    
    Returns:
    
    the list of Voxels
  - listValues
```
public abstract ArrayUtil listValues(ImageHandler ima)
```
    Outputs the list of Voxels values using intensity image
    
    Parameters:
    
    ima - the intensity image
    
    Returns:
    
    a array of values
  - listValues
```
public abstract ArrayUtil listValues(ImageHandler ima,
                                     float thresh)
```
    Outputs the list of Voxels values using intensity image above a fixed threshold
    
    Parameters:
    
    ima - the intensity image
    
    Returns:
    
    a array of values
  - listVoxels
```
public abstract java.util.List<Voxel3D> listVoxels(ImageHandler ima,
                                                   double thresh)
```
    List Voxels in the image with values > threshold
    
    Parameters:
    
    ima - The image with values
    
    thresh - the threshold
    
    Returns:
    
    the list of Voxels with values > threshold
  - listVoxels
```
public abstract java.util.List<Voxel3D> listVoxels(ImageHandler ima,
                                                   double thresh0,
                                                   double thres1)
```
    List Voxels in the image with values > threshold0 and < threshold1
    
    Parameters:
    
    ima - The image with values
    
    thresh0 - the min threshold
    
    thres1 - the max threshold
    
    Returns:
    
    the list of Voxels with values > threshold
  - listVoxelsByDistance
```
public java.util.List<Voxel3D> listVoxelsByDistance(Point3D P0,
                                                    double dist0,
                                                    double dist1,
                                                    boolean contourOnly)
```
    List Voxels in the image with with distances in specific range from a reference point
    
    Parameters:
    
    P0 - the reference point
    
    dist0 - the min distance
    
    dist1 - the max distance
    
    contourOnly - lsit only voxels from the contour of the object
    
    Returns:
  - getObject3DVoxels
```
public Object3DVoxels getObject3DVoxels()
```
    Convert the object to voxels (if necessary)
    
    Returns:
    
    the object as a voxels object
  - getObject3DSurface
```
public Object3DSurface getObject3DSurface()
```
    Convert the object to surface (if necessary)
    
    Returns:
    
    the object as a voxels object
  - pcColoc
```
public double pcColoc(Object3D obj)
```
    Percentage of colocalisation between two objects relative to this object
    
    Parameters:
    
    obj - the other object
    
    Returns:
    
    the percentage of colocalisation (0-100)
  - draw
```
public abstract void draw(ObjectCreator3D obj,
                          int col)
```
    drawing inside an objectCreator
    
    Parameters:
    
    obj - the object creator
    
    col - the color(grey level)
  - draw
```
public abstract boolean draw(ByteProcessor mask,
                             int z,
                             int col)
```
    Deprecated. use Object3D-IJUtils drawing inside a 2D byteprocessor
    
    Parameters:
    
    mask - the byte processor
    
    z - the z slice
    
    col - the color(grey level)
    
    Returns:
  - draw
```
public abstract void draw(ImageStack mask,
                          int col)
```
    Deprecated. use Object3D-IJUtils drawing inside an imagestack
    
    Parameters:
    
    mask - the image
    
    col - the color(grey level)
  - draw
```
public abstract void draw(ImageHandler mask,
                          float val)
```
    drawing inside an ImageHandler
    
    Parameters:
    
    mask - the image
    
    val - the real value
  - drawAt
```
public void drawAt(ImageHandler mask,
                   int col,
                   Point3D center)
```
  - draw
```
public abstract void draw(ImageHandler mask,
                          int col,
                          int tx,
                          int ty,
                          int tz)
```
    Parameters:
    
    mask -
    
    col -
    
    tx -
    
    ty -
    
    tz -
  - draw
```
public void draw(ImageHandler mask)
```
    Drawing inside an image, with default value = object value
    
    Parameters:
    
    mask - image
  - drawLink
```
public void drawLink(ImageHandler mask,
                     Object3D other,
                     int col)
```
    Drawing links between two objects
    
    Parameters:
    
    mask -
    
    other -
    
    col -
  - draw
```
public abstract void draw(ImageStack mask,
                          int r,
                          int g,
                          int b)
```
    Deprecated. use Object3D-IJUtils drawing inside an imagestack, in rgb color
    
    Parameters:
    
    mask - the imagestack
    
    r - red value
    
    g - greeen value
    
    b - blue value
  - createRoi
```
public abstract Roi createRoi(int z)
```
    Deprecated. use Object3D-IJUtils create a roi for a slice
    
    Parameters:
    
    z - the z slice
    
    Returns:
    
    the contour roi in slice z
  - getConvexPolygonRoi
```
public PolygonRoi getConvexPolygonRoi(int z)
```
  - init
```
public void init()
```
    Init default values and compute contours and center
  - getContours
```
public java.util.LinkedList<Voxel3D> getContours()
```
    return the list of contour voxels
    
    Returns:
    
    the list of contour voxels
  - getValue
```
public int getValue()
```
    Value of the Object3D
    
    Returns:
    
    value
  - setValue
```
public void setValue(int v)
```
    Sets the value attribute of the Object3D object
    
    Parameters:
    
    v - The new value value
  - getXmin
```
public int getXmin()
```
    Gets the xmin attribute of the Object3D
    
    Returns:
    
    The xmin value
  - getYmin
```
public int getYmin()
```
    Gets the ymin attribute of the Object3D
    
    Returns:
    
    The ymin value
  - getZmin
```
public int getZmin()
```
    Gets the zmin attribute of the Object3D
    
    Returns:
    
    The zmin value
  - getXmax
```
public int getXmax()
```
    Gets the xmax attribute of the Object3D
    
    Returns:
    
    The xmax value
  - getYmax
```
public int getYmax()
```
    Gets the ymax attribute of the Object3D
    
    Returns:
    
    The ymax value
  - getZmax
```
public int getZmax()
```
    Gets the zmax attribute of the Object3D
    
    Returns:
    
    The zmax value
  - getBoundingBox
```
public int[] getBoundingBox()
```
    Get the bounding box of the object (Xmin, Xmax, Ymin, Ymax, Zmin, Zmax)
    
    Returns:
    
    the coordinates of the bounding box
  - getCenterX
```
public double getCenterX()
```
    x coordinate of the center
    
    Returns:
    
    x center value
  - getCenterY
```
public double getCenterY()
```
    y coordinate of the center
    
    Returns:
    
    y center value
  - getCenterZ
```
public double getCenterZ()
```
    z coordinate of the center
    
    Returns:
    
    z center value
  - isEmpty
```
public boolean isEmpty()
```
    Returns:
  - getIntegratedDensity
```
public double getIntegratedDensity(ImageHandler ima)
```
    integrated density of the Object3D in an image
    
    Parameters:
    
    ima - the image
    
    Returns:
    
    the sum of pixels values
  - getIntegratedDensity
```
public double getIntegratedDensity(ImageHandler ima,
                                   ImageHandler mask)
```
  - getMassCenterX
```
public double getMassCenterX(ImageHandler ima)
```
    x coordinate of the center of mass in an image
    
    Parameters:
    
    ima - the image
    
    Returns:
    
    x coordinate of mass center
  - setNewCenter
```
public void setNewCenter(double x,
                         double y,
                         double z)
```
    Parameters:
    
    x -
    
    y -
    
    z -
  - setNewCenter
```
public void setNewCenter(Object3D obj)
```
  - setNewCenter
```
public void setNewCenter(Vector3D newCenter)
```
  - translate
```
public abstract void translate(double x,
                               double y,
                               double z)
```
    Parameters:
    
    x -
    
    y -
    
    z -
  - translate
```
public void translate(Vector3D V)
```
    Parameters:
    
    V -
  - getMassCenterY
```
public double getMassCenterY(ImageHandler ima)
```
    u coordinate of the center of mass in an image
    
    Parameters:
    
    ima - the image
    
    Returns:
    
    y coordinate of mass center
  - getMassCenterZ
```
public double getMassCenterZ(ImageHandler ima)
```
    z coordinate of the center of mass in an image
    
    Parameters:
    
    ima - the image
    
    Returns:
    
    z coordinate of mass center
  - getCenterAsVector
```
public Vector3D getCenterAsVector()
```
    Gets the center attribute of the Object3D object
    
    Returns:
    
    The center value
  - getCenterAsVectorUnit
```
public Vector3D getCenterAsVectorUnit()
```
    Gets the center attribute of the Object3D object
    
    Returns:
    
    The center value
  - getCenterAsPoint
```
public Point3D getCenterAsPoint()
```
    Gets the center attribute of the Object3D object
    
    Returns:
    
    The center value
  - getCenterAsArray
```
public double[] getCenterAsArray()
```
    Returns:
  - getAreaPixels
```
public double getAreaPixels()
```
    the area of the Object3D (in pixels)
    
    Returns:
    
    the area value
  - getAreaUnit
```
public double getAreaUnit()
```
    Gets the areaUnit attribute of the Object3D object
    
    Returns:
    
    The areaUnit value
  - getCompactness
```
public double getCompactness(boolean useUnit)
```
    Gets the compactness attribute of the Object3D (unit) related to sphericity
    
    Parameters:
    
    useUnit - use calibration about area and volumes
    
    Returns:
    
    The compactness value
  - getCompactness
```
public double getCompactness()
```
  - getSphericity
```
public double getSphericity()
```
  - getSphericity
```
public double getSphericity(boolean useUnit)
```
    Gets the sphericity attribute of the Object3D (unit) related to compactness
    
    Returns:
    
    The compactness value
  - getRatioBox
```
public double getRatioBox()
```
    Gets the ration between volume and volume of the bounding box (in units)
    
    Returns:
    
    The ratioBox value
  - getRatioEllipsoid
```
public double getRatioEllipsoid()
```
    Gets the ration between volume and volume of the ellipsoid (in units)
    
    Returns:
    
    The ratio value
  - getVolumeBoundingBoxPixel
```
public double getVolumeBoundingBoxPixel()
```
    the volume of the bounding box
    
    Returns:
    
    the volume
  - getVolumeBoundingBoxOrientedPixel
```
public double getVolumeBoundingBoxOrientedPixel()
```
    the volume of the oriented bounding box FIXME computing of oriented box
    
    Returns:
    
    the volume
  - getBoundingOriented
```
public java.util.ArrayList<Voxel3D> getBoundingOriented()
```
  - getVolumeEllipseUnit
```
public double getVolumeEllipseUnit()
```
    The volume of the approximated ellipsoid in unit the main radius is DCMax
    
    Returns:
    
    the volume of the ellipsoid
  - computeEigen
```
protected void computeEigen()
```
    Constructor for the computeEigen object
  - getMatrixAxes
```
public Matrix getMatrixAxes()
```
    Gets the main axes vectors as a matrix
    
    Returns:
    
    The matrix, e1 is main axis
  - getValueAxis
```
public double getValueAxis(int order)
```
    Gets the valueAxis attribute of the Object3D object (unit)
    
    Parameters:
    
    order - the order of the value
    
    Returns:
    
    The valueAxis value
  - getMainAxis
```
public Vector3D getMainAxis()
```
    Gets the mainAxis attribute of the Object3D object (unit)
    
    Returns:
    
    The mainAxis value
  - getVectorAxis
```
public Vector3D getVectorAxis(int order)
```
    Gets the Axis attribute of the Object3D object (unit)
    
    Parameters:
    
    order - the order of the axis
    
    Returns:
    
    The mainAxis value
  - getRadiusMoments
```
public double getRadiusMoments(int order)
```
    Parameters:
    
    order -
    
    Returns:
  - getMainElongation
```
public double getMainElongation()
```
    Gets the main elongation of the object
    
    Returns:
    
    The main elongation
  - getMedianElongation
```
public double getMedianElongation()
```
    Gets the flatness of the object
    
    Returns:
    
    The median elongation (flatness)
  - computeContours
```
public void computeContours(ImageHandler ima)
```
    The contours is given in an image (see OC3D)
    
    Parameters:
    
    ima - the image with labelled contours
  - getDistCenterMin
```
public double getDistCenterMin()
```
    the minimum distance between center and contours
    
    Returns:
    
    the min distance(in real unit)
  - getDistCenterMax
```
public double getDistCenterMax()
```
    the maximum distance between center and contours
    
    Returns:
    
    the max distance(in real unit)
  - getDistCenterMean
```
public double getDistCenterMean()
```
    the average distance between center and contours
    
    Returns:
    
    the mean distance(in real unit)
  - getDistCenterSigma
```
public double getDistCenterSigma()
```
    the sigma value for distances between center and contours
    
    Returns:
    
    the SD distance
  - getDistCenterMinPixel
```
public double getDistCenterMinPixel()
```
    the minimum distance between center and contours
    
    Returns:
    
    the min distance(in pixel)
  - getDistCenterMaxPixel
```
public double getDistCenterMaxPixel()
```
    the maximum distance between center and contours
    
    Returns:
    
    the max distance(in pixel)
  - getDistCenterMeanPixel
```
public double getDistCenterMeanPixel()
```
    the average distance between center and contours
    
    Returns:
    
    the mean distance(in real unit)
  - getDistCenterSigmaPixel
```
public double getDistCenterSigmaPixel()
```
    the sigma value for distances between center and contours
    
    Returns:
    
    the SD distance
  - centerInside
```
public boolean centerInside()
```
    Returns:
  - getFeret
```
public double getFeret()
```
    Gets the feret diameter of the object (unit)
    
    Returns:
    
    The feret value
  - getFeretVoxel1
```
public Voxel3D getFeretVoxel1()
```
    Gets the first feret voxel of the object (unit)
    
    Returns:
    
    The feret voxel
  - getFeretVoxel2
```
public Voxel3D getFeretVoxel2()
```
    Gets the second feret voxel of the object (unit)
    
    Returns:
    
    The feret voxel
  - toString
```
public java.lang.String toString()
```
    Display information
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    text
  - distBorderUnit
```
public double distBorderUnit(Object3D other)
```
    the minimum distance between two objets (in real distance) computed on the contours pixels
    
    Parameters:
    
    other - the other Object3D
    
    Returns:
    
    the minimum distance
  - distHausdorffUnit
```
public double distHausdorffUnit(Object3D other)
```
  - distBorderPixel
```
public double distBorderPixel(Object3D other)
```
    the minimum distance between two objets (in real distance) computed on the contours pixels
    
    Parameters:
    
    other - the other Object3D
    
    Returns:
    
    the minimum distance
  - distBorderUnit
```
public double distBorderUnit(Point3D point0,
                             Object3D other,
                             Point3D point1,
                             boolean opposite)
```
    The border to border distance along a direction (EXPERIMENTAL)
    
    Parameters:
    
    point0 -
    
    other - the other object
    
    opposite -
    
    point1 -
    
    Returns:
    
    the border to border distance
  - distCenterUnit
```
public double distCenterUnit(Object3D autre)
```
    distance from center to center (in real distance)
    
    Parameters:
    
    autre - the other Object3D (has the same resolution !)
    
    Returns:
    
    distance
  - distCenterPixel
```
public double distCenterPixel(Object3D other)
```
    distance from center to center (in pixel)
    
    Parameters:
    
    other - the other Object3D
    
    Returns:
    
    distance
  - distCenter2DUnit
```
public double distCenter2DUnit(Object3D autre)
```
    2D distance from center to center (in real distance)
    
    Parameters:
    
    autre - the other Object3D
    
    Returns:
    
    distance
  - distCenterBorderUnit
```
public double distCenterBorderUnit(Object3D autre)
```
    Distance center of this object to the border of the other
    
    Parameters:
    
    autre - Other object
    
    Returns:
    
    Min distance between center and border ot other object
  - distPixelBorder
```
public double distPixelBorder(Point3D P)
```
    Parameters:
    
    P -
    
    Returns:
  - distPixelBorderUnit
```
public double distPixelBorderUnit(double x,
                                  double y,
                                  double z)
```
    Distance from a point to the border of the object
    
    Parameters:
    
    x - x coordinate of the point
    
    y - y coordinate of the point
    
    z - z coordinate of the point
    
    Returns:
    
    The shortest distance
  - distPixelBorderUnit
```
public double distPixelBorderUnit(double x,
                                  double y,
                                  double z,
                                  Vector3D V)
```
    Distance from a point along a direction to the border of the object
    
    Parameters:
    
    x - x coordinate of the point in pixel
    
    y - y coordinate of the point in pixel
    
    z - z coordinate of the point in pixel
    
    V - the direction vector
    
    Returns:
    
    The shortest distance in unit
  - distPixelCenter
```
public double distPixelCenter(double x,
                              double y,
                              double z)
```
    The distance between center and a point with coordinates
    
    Parameters:
    
    x - x-coordinate of the point
    
    y - y-coordinate of the point
    
    z - z-coordinate of the point
    
    Returns:
    
    the distance (in unit)
  - distPixelCenter
```
public double distPixelCenter(Point3D P)
```
    The distance between center and a Point3D
    
    Parameters:
    
    P - the point
    
    Returns:
    
    the distance (in unit)
  - getCenterUnit
```
public Vector3D getCenterUnit()
```
    Gets the centerUnit attribute of the Object3D object
    
    Returns:
    
    The centerUnit value
  - isContour
```
public boolean isContour(Voxel3D vox)
```
    Parameters:
    
    vox -
    
    Returns:
  - insideBounding
```
public boolean insideBounding(double x,
                              double y,
                              double z)
```
    test if the point is inside the bounding box of the object
    
    Parameters:
    
    x - x coordinate of the point
    
    y - y coordinate of the point
    
    z - z coordinate of the point
    
    Returns:
    
    true or false
  - insideBounding
```
public boolean insideBounding(float x,
                              float y,
                              float z)
```
    test if the point is inside the bounding box of the object
    
    Parameters:
    
    x - x coordinate of the point
    
    y - y coordinate of the point
    
    z - z coordinate of the point
    
    Returns:
    
    true or false
  - insideBounding
```
public boolean insideBounding(double x,
                              double y,
                              double z,
                              int rx,
                              int ry,
                              int rz)
```
    Parameters:
    
    x -
    
    y -
    
    z -
    
    rx -
    
    ry -
    
    rz -
    
    Returns:
  - inside
```
public boolean inside(Point3D P)
```
  - insideOne
```
public boolean insideOne(java.util.ArrayList<Point3D> markers)
```
  - insideAll
```
public boolean insideAll(java.util.ArrayList<Point3D> markers)
```
  - inside
```
public boolean inside(double x,
                      double y,
                      double z)
```
    test if the point is inside the object
    
    Parameters:
    
    x - x-coordinate of the point
    
    y - y-coordinate of the point
    
    z - z-coordinate of the point
    
    Returns:
    
    true is point inside object
  - includesBox
```
public boolean includesBox(Object3D autre)
```
    Test if the bouding boxes intersect
    
    Parameters:
    
    autre - the othe object
    
    Returns:
    
    true or false
  - getIntersectionBox
```
protected int[] getIntersectionBox(Object3D other)
```
    Parameters:
    
    other -
    
    Returns:
  - overlapBox
```
public boolean overlapBox(Object3D other)
```
    Parameters:
    
    other -
    
    Returns:
  - disjointBox
```
public boolean disjointBox(Object3D other)
```
    Parameters:
    
    other -
    
    Returns:
  - createIntersectionImage
```
public ImageHandler createIntersectionImage(Object3D other,
                                            int val1,
                                            int val2,
                                            int border)
```
    Create an intersection image around two objects
    
    Parameters:
    
    other - the Other object
    
    val1 - the value for this object
    
    val2 - the value for other object
    
    border - the border around box
    
    Returns:
    
    the image with 3 values (val1 for this, val2 for other, val1+val2 for intersection)
  - createIntersectionImage
```
public ImageHandler createIntersectionImage(Object3D other,
                                            int val1,
                                            int val2)
```
    Create an intersection image around two objects (with no extra borders)
    
    Parameters:
    
    other - the Other object
    
    val1 - the value for this object
    
    val2 - the value for other object
    
    Returns:
    
    the image with 3 values (val1 for this, val2 for other, val1+val2 for intersection)
  - getIntersectionObject
```
public Object3DVoxels getIntersectionObject(Object3D other)
```
    Get the intersection voxels as a 3D object
    
    Parameters:
    
    other - The other object
    
    Returns:
    
    The object with intersection voxels (or null if objects are disjoint)
  - surfaceContact
```
public int[] surfaceContact(Object3D other,
                            double dist_max)
```
    Get the contact surfaces between two objects, outside voxels < dist and number of border voxels of this object included in the objectB
    
    Parameters:
    
    other - the objectB object
    
    dist_max - distance max (in pixel) between two contour points of the two objects
    
    Returns:
    
    int array with : nb ofcontours points below distance max to contours points in objectB object AND nb of voxel of this object inside the objectB one
  - edgeContact
```
public int edgeContact(Object3D other,
                       int distSquareMax)
```
    Parameters:
    
    other - object
    
    distSquareMax - object maximum square distance between two voxels (0 for coloc, 1 for side contact, >1 for diagonal contact
    
    Returns:
    
    nb ofcontours voxels of first object at a distance inferior to dist_square_max in pixels
  - edgeImage
```
public boolean edgeImage(ImageHandler img,
                         boolean edgeXY,
                         boolean edgeZ)
```
  - radiusCenter
```
public double radiusCenter(Object3D obj)
```
    the radius of the object towards another object
    
    Parameters:
    
    obj - the other object
    
    Returns:
    
    the radius (in real units)
  - radiusCenter
```
public double radiusCenter(Object3D obj,
                           boolean opposite)
```
    the radius of the object towards another object, in forward or opposite direction
    
    Parameters:
    
    obj - the other object
    
    opposite - opposite or forward direction
    
    Returns:
    
    the radius (in real units)
  - radiusCenter
```
public double radiusCenter(Vector3D V)
```
    the radius along a direction
    
    Parameters:
    
    V - the direction
    
    Returns:
    
    the radius (in real units)
  - radiusPixel
```
public double radiusPixel(double x,
                          double y,
                          double z)
```
    the radius towards a point
    
    Parameters:
    
    x - the x-coordinate of the point
    
    y - the y-coordinate of the point
    
    z - the z-coordinate of the point
    
    Returns:
    
    the radius (in real units)
  - vectorBorderBorder
```
public Vector3D vectorBorderBorder(Object3D other)
```
    Gets the areaUnit attribute of the Object3D object
    
    Parameters:
    
    other -
    
    Returns:
    
    The areaUnit value
  - VoxelsBorderBorder
```
public Voxel3D[] VoxelsBorderBorder(Object3D other)
```
    Return the two voxels defining the border-border distance
    
    Parameters:
    
    other - The other object
    
    Returns:
    
    The two voxels(from this object, from other object)
  - vectorBorderBorder
```
public Vector3D vectorBorderBorder(Point3D point0,
                                   Object3D other,
                                   Point3D point1,
                                   boolean opposite)
```
    The vector between V0 and V1 : V0 is the point on border of object from point0 along direction V1 is the point on border of other object from point1 along opposite direction
    
    Parameters:
    
    point0 - the first point on this object
    
    other - the other object
    
    point1 - the second point on other object
    
    opposite -
    
    Returns:
    
    The difference vector between the two border points
  - vectorCenterBorder
```
public Vector3D vectorCenterBorder(Object3D other)
```
    The vector between the center of this object and the border of the other object
    
    Parameters:
    
    other - the othe object
    
    Returns:
    
    The difference vector between the two closest points
  - vectorPixelBorder
```
public Vector3D vectorPixelBorder(Vector3D V)
```
    Vector between a voxel defined by a vector and the closest border
    
    Parameters:
    
    V - The 3D point defined as a vector
    
    Returns:
    
    the vector
  - getPixelBorder
```
public Voxel3D getPixelBorder(double x,
                              double y,
                              double z)
```
  - vectorPixelBorder
```
public Vector3D vectorPixelBorder(double x,
                                  double y,
                                  double z)
```
    Vector between a pixel and the closest border
    
    Parameters:
    
    x - x coordinate of the pixel
    
    y - y coordinate of the pixel
    
    z - z coordinate of the pixel
    
    Returns:
    
    the vector
  - vectorPixelBorder
```
public Vector3D vectorPixelBorder(double x,
                                  double y,
                                  double z,
                                  Vector3D V)
```
    Vector from a point along a direction to the border of the object The distance is the distance to the point where there is a change in the object appartenance (inside / outside)
    
    Parameters:
    
    x - x coordinate of the point
    
    y - y coordinate of the point
    
    z - z coordinate of the point
    
    V - the direction vector
    
    Returns:
    
    The shortest distance Vector
  - pointPixelBorder
```
public Point3D pointPixelBorder(double x,
                                double y,
                                double z,
                                Vector3D V)
```
    Vector from a point along a direction to the border of the object
    
    Parameters:
    
    x - x coordinate of the point
    
    y - y coordinate of the point
    
    z - z coordinate of the point
    
    V - the direction vector
    
    Returns:
    
    The shortest distance Vector
  - vectorPixelUnitBorder
```
public Vector3D vectorPixelUnitBorder(Vector3D V)
```
    vector between a point and the border the vector is given is real units
    
    Parameters:
    
    V - the vector (to describe the point)
    
    Returns:
    
    vector between the point and the border
  - vectorPixelUnitBorder
```
public Vector3D vectorPixelUnitBorder(Vector3D V,
                                      Vector3D dir)
```
    vector between a point and the border along a direction the point is given is real units
    
    Parameters:
    
    V - the vector (to describe the point)
    
    dir - the direction
    
    Returns:
    
    vector between the point and the border
  - vectorPixelUnitBorder
```
public Vector3D vectorPixelUnitBorder(double x,
                                      double y,
                                      double z)
```
    vector between a pixel and the border the point is given is real units
    
    Parameters:
    
    x - the x-coordinate of the point
    
    y - the y-coordinate of the point
    
    z - the z-coordinate of the point
    
    Returns:
    
    vector between the point and the border
  - vectorPixelUnitBorder
```
public Vector3D vectorPixelUnitBorder(double x,
                                      double y,
                                      double z,
                                      Vector3D dir)
```
    vector between a pixel and the border, along a direction the vector is given is real units
    
    Parameters:
    
    x - the x-coordinate of the point
    
    y - the y-coordinate of the point
    
    z - the z-coordinate of the point
    
    dir - the direction
    
    Returns:
    
    vector between the point and the border
  - angle
```
public double angle(Object3D a,
                    Object3D b)
```
    Angle between (a, this, b) with real coordinates
    
    Parameters:
    
    a - Object3D a
    
    b - Object3D b
    
    Returns:
    
    Angle in degrees
  - getPixMeanValue
```
public double getPixMeanValue(ImageHandler ima)
```
    Gets the meanPixValue attribute of the Object3D object
    
    Parameters:
    
    ima -
    
    Returns:
    
    The meanPixValue value
  - getPixMeanValueContour
```
public double getPixMeanValueContour(ImageHandler ima)
```
  - getPixMedianValue
```
public double getPixMedianValue(ImageHandler ima)
```
  - getPixModeValue
```
public double getPixModeValue(ImageHandler ima)
```
  - getPixModeNonZero
```
public double getPixModeNonZero(ImageHandler ima)
```
  - getMeanPixValueAroundBarycenter
```
public double getMeanPixValueAroundBarycenter(boolean massCenter,
                                              ImageInt objectMap,
                                              ImageHandler ima,
                                              double radXY,
                                              double radZ)
```
    Parameters:
    
    massCenter -
    
    objectMap -
    
    ima -
    
    radXY -
    
    radZ -
    
    Returns:
  - getPixMaxValue
```
public double getPixMaxValue(ImageHandler ima)
```
    Gets the pixMaxValue attribute of the Object3D object
    
    Parameters:
    
    ima -
    
    Returns:
    
    The pixMaxValue value
  - getPixCenterValue
```
public double getPixCenterValue(ImageHandler ima)
```
  - getPixMinValue
```
public double getPixMinValue(ImageHandler ima)
```
    Gets the pixMinValue attribute of the Object3D object
    
    Parameters:
    
    ima -
    
    Returns:
    
    The pixMinValue value
  - getNumbering
```
public int[] getNumbering(ImageHandler ima)
```
    Will count the number of different objects within this object *
    
    Parameters:
    
    ima - A labelled image
    
    Returns:
    
    the number of objects and the volume occupied by the objects
  - resetQuantifImage
```
public void resetQuantifImage()
```
  - getPixStdDevValue
```
public double getPixStdDevValue(ImageHandler ima)
```
    Gets the SD of pixels in object
    
    Parameters:
    
    ima - the 3D image
    
    Returns:
    
    The sigma value
  - createSegImageMini2D
```
public ImageInt createSegImageMini2D(int val,
                                     int borderSize)
```
    Parameters:
    
    val -
    
    borderSize -
    
    Returns:
  - createSegImage
```
public ImageHandler createSegImage(int xmi,
                                   int ymi,
                                   int zmi,
                                   int xma,
                                   int yma,
                                   int zma,
                                   int val)
```
    Parameters:
    
    xmi -
    
    ymi -
    
    zmi -
    
    xma -
    
    yma -
    
    zma -
    
    val -
    
    Returns:
  - createSegImage
```
public ImageHandler createSegImage(int bx,
                                   int by,
                                   int bz)
```
  - getVoxels
```
public abstract java.util.List<Voxel3D> getVoxels()
```
    Get the list of voxels of the object
    
    Returns:
    
    the list of voxels
  - saveObject
```
public abstract void saveObject(java.lang.String path)
```
    Parameters:
    
    path -
  - saveInfo
```
protected void saveInfo(java.io.BufferedWriter bf)
                 throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - loadInfo
```
protected java.lang.String loadInfo(java.io.BufferedReader bf)
                             throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - computeMeshSurface
```
public java.util.List computeMeshSurface(boolean calibrated)
```
    Deprecated. use Object3D-IJUtils
    
    Parameters:
    
    calibrated -
    
    Returns:
  - includesMarkersNone
```
public boolean includesMarkersNone(ImageInt imageMarkers)
```
  - includesMarkersOneOnly
```
public boolean includesMarkersOneOnly(ImageInt imageMarkers)
```
  - includesMarkersOneMore
```
public boolean includesMarkersOneMore(ImageInt imageMarkers)
```
  - includedInZonesNone
```
public boolean includedInZonesNone(ImageInt imageZones)
```
  - includedInZonesOneOnly
```
public boolean includedInZonesOneOnly(ImageInt imageZones)
```
  - includedInZonesOneMore
```
public boolean includedInZonesOneMore(ImageInt imageZones)
```
  - includes
```
public boolean includes(Object3D obj)
```
    Parameters:
    
    obj -
    
    Returns:
  - hasOneVoxelColoc
```
public abstract boolean hasOneVoxelColoc(Object3D obj)
```
    Parameters:
    
    obj -
    
    Returns:
  - hasOneVoxelValueRange
```
public abstract boolean hasOneVoxelValueRange(ImageHandler img,
                                              int t0,
                                              int t1)
```
  - getColoc
```
public abstract int getColoc(Object3D obj)
```
    Parameters:
    
    obj -
    
    Returns:
  - touchBorders
```
public boolean touchBorders(ImageHandler img,
                            boolean Z)
```
  - touchBorders
```
public boolean touchBorders(ImagePlus img,
                            boolean Z)
```
    Deprecated. use Object3D-IJUtils
    
    Parameters:
    
    img -
    
    Z -
    
    Returns:
  - b_closed
```
public boolean b_closed(float radX,
                        float radY,
                        float radZ)
```
    Parameters:
    
    radX -
    
    radY -
    
    radZ -
    
    Returns:
  - b_open
```
public boolean b_open(float radX,
                      float radY,
                      float radZ)
```
    Parameters:
    
    radX -
    
    radY -
    
    radZ -
    
    Returns:
  - regular
```
public boolean regular(float radX,
                       float radY,
                       float radZ)
```
    Parameters:
    
    radX -
    
    radY -
    
    radZ -
    
    Returns:
  - getDilatedObject
```
public Object3DVoxels getDilatedObject(float radX,
                                       float radY,
                                       float radZ)
```
    Parameters:
    
    radX -
    
    radY -
    
    radZ -
    
    Returns:
  - getErodedObject
```
public Object3DVoxels getErodedObject(float radX,
                                      float radY,
                                      float radZ)
```
    Parameters:
    
    radX -
    
    radY -
    
    radZ -
    
    Returns:
  - getClosedObject
```
public Object3DVoxels getClosedObject(float radX,
                                      float radY,
                                      float radZ)
```
    Parameters:
    
    radX -
    
    radY -
    
    radZ -
    
    Returns:
  - getOpenedObject
```
public Object3DVoxels getOpenedObject(float radX,
                                      float radY,
                                      float radZ)
```
    Parameters:
    
    radX -
    
    radY -
    
    radZ -
    
    Returns:
  - getLayerObject
```
public Object3DVoxels getLayerObject(float r1,
                                     float r2)
```
  - getLayerEVFObject
```
public Object3DVoxels getLayerEVFObject(ImageInt mask,
                                        float ratio)
```
  - getLayerEVFObject
```
public Object3DVoxels getLayerEVFObject(Object3D mask,
                                        float ratio)
```
  - getEllipsoid
```
public Object3DVoxels getEllipsoid()
```
  - getConvexSurface
```
public Object3DSurface getConvexSurface()
```
    Returns:
  - getConvexObject
```
public Object3DVoxels getConvexObject(boolean multi)
```
    Parameters:
    
    multi - multiprocessor
    
    Returns:
  - getConvexObject
```
public Object3DVoxels getConvexObject()
```
    Returns:
  - compareTo
```
public int compareTo(Object3D o)
```
    Specified by:
    
    compareTo in interface java.lang.Comparable<Object3D>

Class Object3D

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MEASURE_NONE

MEASURE_VOLUME_PIX

MEASURE_VOLUME_UNIT

MEASURE_MAIN_ELONGATION

MEASURE_COMPACTNESS_VOXELS

MEASURE_COMPACTNESS_UNITS

MEASURE_AREA_PIX

MEASURE_AREA_UNIT

MEASURE_DC_AVG

MEASURE_DC_SD

MEASURE_INTENSITY_AVG

MEASURE_INTENSITY_SD

MEASURE_INTENSITY_MIN

MEASURE_INTENSITY_MAX

MEASURE_INTENSITY_MEDIAN

s200

verbose

multiThread

compare

name

type

comment

xmin

ymin

zmin

xmax

ymax

zmax

bx

by

bz

cx

cy

cz

areaNbVoxels

areaContactUnit

areaContactVoxels

volume

feret

feret1

feret2

integratedDensity

meanDensity

sigma

pixmin

pixmax

value

contours

kdtreeContours

s110

s101

s020

s011

s002

s300

s210

s201

s030

s120

s021

s003

s102

s012

s111

s400

s040

s004

s220

s202

s022

s121

s112

s211

s103