mcib3d.geom

Class Object3DVoxels

java.lang.Object

mcib3d.geom.Object3D

mcib3d.geom.Object3DVoxels

All Implemented Interfaces:

java.lang.Comparable<Object3D>

Direct Known Subclasses:

Object3DFuzzy, Object3DPoint

public class Object3DVoxels
extends 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 .

An Object3D defined as a list of voxels

Field Summary

Fields inherited from class mcib3d.geom.Object3D

areaContactUnit, areaContactVoxels, areaNbVoxels, bx, by, bz, comment, compare, contours, currentQuantifImage, cx, cy, cz, eigen, feret, feret1, feret2, integratedDensity, kdtreeContours, labelImage, meanDensity, MEASURE_AREA_PIX, MEASURE_AREA_UNIT, MEASURE_COMPACTNESS_UNITS, MEASURE_COMPACTNESS_VOXELS, MEASURE_DC_AVG, MEASURE_DC_SD, MEASURE_INTENSITY_AVG, MEASURE_INTENSITY_MAX, MEASURE_INTENSITY_MEDIAN, MEASURE_INTENSITY_MIN, MEASURE_INTENSITY_SD, MEASURE_MAIN_ELONGATION, MEASURE_NONE, MEASURE_VOLUME_PIX, MEASURE_VOLUME_UNIT, miniLabelImage, multiThread, name, pixmax, pixmin, resXY, resZ, s002, s003, s004, s011, s012, s013, s020, s021, s022, s030, s031, s040, s101, s102, s103, s110, s111, s112, s120, s121, s130, s200, s201, s202, s210, s211, s220, s300, s301, s310, s400, sigma, type, units, value, verbose, volume, xmax, xmin, ymax, ymin, zmax, zmin

Constructor Summary

Constructors

Constructor and Description
Object3DVoxels()
Object3DVoxels(ImageHandler ima)
Object3DVoxels(ImageHandler imaSeg, ImageHandler imaRaw)
Object3DVoxels(ImageHandler ima, int val) constructor
Object3DVoxels(ImagePlus plus, int val) Deprecated. use Object3D-IJUtils Constructor for the Object3D object
Object3DVoxels(ImageStack stack, int val) Deprecated. use Object3D-IJUtils Constructor for the Object3D object
Object3DVoxels(int val)
Object3DVoxels(java.util.List<Voxel3D> al)
Object3DVoxels(Object3D other)
Object3DVoxels(Object3DVoxels other) copy

Method Summary

Modifier and Type	Method and Description
void	addVoxels(java.util.List<Voxel3D> vox)
void	addVoxelsIntersection(java.util.ArrayList<Object3D> objs)
void	addVoxelsIntersection(Object3D ob1, Object3D ob2)
void	addVoxelsUnion(java.util.ArrayList<Object3D> objs)
void	addVoxelsUnion(Object3D ob1, Object3D ob2)
protected void	computeBounding() Compute the bounding box of the object
protected void	computeCenter() Compute the barycenter and the volume
void	computeContours() Compute the contours of the object rad=0.5
protected void	computeMassCenter(ImageHandler ima) Compute the mass center of the object using signal from an image
protected void	computeMassCenter(ImageHandler ima, ImageHandler mask) Compute the mass center of the object using signal from an image and within a mask
protected void	computeMoments2(boolean normalize) Computation of the dispersion tensor with units value
void	computeMoments3() Compute the moments of the object, order 3
void	computeMoments4() Compute the moments of the object, order 4
void	computeMomentsInertia() Computation of the inertia tensor with units value
Object3DVoxels	copyObject(int newLabel)
void	createEllipsoidPixel(int cx, int cy, int cz, float rx, float ry, float rz)
Roi	createRoi(int z) Deprecated. use Object3D-IJUtils Constructor for the createRoi object
void	createSphereUnit(float cx, float cy, float cz, float rad)
Object3DVoxels	dilate(float dilateSize, ImageInt mask, int nbCPUs)
boolean	draw(ByteProcessor mask, int z, int col) Deprecated. use Object3D-IJUtils Draw inside a particular Z
void	draw(ImageHandler mask, float col) drawing inside an ImageHandler
void	draw(ImageHandler mask, int col, int tx, int ty, int tz)
void	draw(ImageStack mask, int col) Deprecated. use Object3D-IJUtils
void	draw(ImageStack mask, int r, int g, int b) Deprecated. use Object3D-IJUtils
void	draw(ObjectCreator3D obj, int col) Draw the pixel inside a creator
void	drawContours(ObjectCreator3D ima, int col)
void	drawContoursXY(ObjectCreator3D ima, int z, int col)
double	getAreaPixelsCorrected()
int	getColoc(Object3D obj)
int	getColocVoxels(Object3D obj)
double	getCompactnessCorrected()
java.util.List<Object3DVoxels>	getConnexComponents()
double	getDiscreteCompactness()
Voxel3D	getFirstVoxel()
Object3DVoxels	getInterior3DFill()
Voxel3D	getPixelMax(ImageHandler ima) compute the voxel with maximum value in an image
double	getPixMedianValue(ImageHandler img)
Voxel3D	getRandomVoxel(java.util.Random ra) Get a random voxel in the object
double	getSphericityCorrected()
float[]	getValueArray(ImageHandler im)
protected java.util.List<Voxel3D>	getVoxelInsideBoundingBox(int[] boundingBox)
java.util.List<Voxel3D>	getVoxels() Get the list of voxels of the object
boolean	hasOneVoxelColoc(Object3D obj)
boolean	hasOneVoxelValueRange(ImageHandler img, int t0, int t1)
boolean	isConnex()
ArrayUtil	listValues(ImageHandler ima) Outputs the list of Voxels values using intensity image
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, double threshold) List Voxels in the image with values > threshold
java.util.List<Voxel3D>	listVoxels(ImageHandler ima, double thresholdLow, double thresholdHigh) List Voxels in the image with values > threshold0 and < threshold1
java.util.List<java.lang.Float>	listVoxels(ImageHandler ima, int newCenterX, int newCenterY, int newCenterZ)
void	loadObject(java.lang.String path, java.lang.String name)
double	pcColoc2(java.util.ArrayList<Object3DVoxels> objs)
void	removeVoxels(int threshold)
void	rotate(Vector3D Axis, double angle)
void	saveObject(java.lang.String path)
void	saveObjectZip(java.lang.String path)
void	setContours(java.util.LinkedList<Voxel3D> contours, double areaUnit)
void	setShowStatus(boolean showStatus)
void	setVoxels(java.util.LinkedList<Voxel3D> al)
void	substractObject(Object3D other)
void	translate(double x, double y, double z)
void	translate(Vector3D trans)

Methods inherited from class mcib3d.geom.Object3D

angle, b_closed, b_open, centerInside, compareTo, computeContours, computeEigen, computeMeshSurface, createIntersectionImage, createIntersectionImage, createSegImage, createSegImage, createSegImageMini2D, disjointBox, distBorderPixel, distBorderUnit, distBorderUnit, distCenter2DUnit, distCenterBorderUnit, distCenterPixel, distCenterUnit, distHausdorffUnit, distPixelBorder, distPixelBorderUnit, distPixelBorderUnit, distPixelCenter, distPixelCenter, draw, drawAt, drawLink, edgeContact, edgeImage, getAreaPixels, getAreaUnit, getArrayValues, getBoundingBox, getBoundingOriented, getCalibration, getCenterAsArray, getCenterAsPoint, getCenterAsVector, getCenterAsVectorUnit, getCenterUnit, getCenterX, getCenterY, getCenterZ, getClosedObject, getComment, getCompactness, getCompactness, getContours, getConvexObject, getConvexObject, getConvexPolygonRoi, getConvexSurface, getDilatedObject, getDistCenterMax, getDistCenterMaxPixel, getDistCenterMean, getDistCenterMeanPixel, getDistCenterMin, getDistCenterMinPixel, getDistCenterSigma, getDistCenterSigmaPixel, getEllipsoid, getErodedObject, getFeret, getFeretVoxel1, getFeretVoxel2, getGeometricInvariants, getHomogeneousInvariants, getIntegratedDensity, getIntegratedDensity, getIntersectionBox, getIntersectionObject, getLabelImage, getLayerEVFObject, getLayerEVFObject, getLayerObject, getMainAxis, getMainElongation, getMassCenterX, getMassCenterY, getMassCenterZ, getMatrixAxes, getMaxLabelImage, getMeanPixValueAroundBarycenter, getMeasure, getMedianElongation, getMoments3D, getMomentsRaw2, getMomentsRaw3, getMomentsRaw4, getName, getNbMoments3D, getNumbering, getObject3DSurface, getObject3DVoxels, getOpenedObject, getPixCenterValue, getPixelBorder, getPixMaxValue, getPixMeanValue, getPixMeanValueContour, getPixMinValue, getPixModeNonZero, getPixModeValue, getPixStdDevValue, getQuantilePixValue, getRadiusMoments, getRatioBox, getRatioEllipsoid, getResXY, getResZ, getSphericity, getSphericity, getType, getUnits, getValue, getValueAxis, getVectorAxis, getVolumeBoundingBoxOrientedPixel, getVolumeBoundingBoxPixel, getVolumeEllipseUnit, getVolumePixels, getVolumeUnit, getXmax, getXmin, getYmax, getYmin, getZmax, getZmin, includedInZonesNone, includedInZonesOneMore, includedInZonesOneOnly, includes, includesBox, includesMarkersNone, includesMarkersOneMore, includesMarkersOneOnly, init, inside, inside, insideAll, insideBounding, insideBounding, insideBounding, insideOne, isContour, isEmpty, listVoxels, listVoxelsByDistance, loadInfo, overlapBox, pcColoc, pcColocSum, pointPixelBorder, radiusCenter, radiusCenter, radiusCenter, radiusPixel, regular, resetQuantifImage, saveInfo, setCalibration, setCalibration, setComment, setLabelImage, setName, setNewCenter, setNewCenter, setNewCenter, setResXY, setResZ, setType, setUnits, setValue, surfaceContact, toString, touchBorders, touchBorders, vectorBorderBorder, vectorBorderBorder, vectorCenterBorder, vectorPixelBorder, vectorPixelBorder, vectorPixelBorder, vectorPixelUnitBorder, vectorPixelUnitBorder, vectorPixelUnitBorder, vectorPixelUnitBorder, VoxelsBorderBorder

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Object3DVoxels

public Object3DVoxels()

Object3DVoxels

public Object3DVoxels(int val)

Object3DVoxels

public Object3DVoxels(ImageHandler ima,
                      int val)

constructor

Parameters:

ima - Segmented image

val - Pixel value of the object

Object3DVoxels

public Object3DVoxels(ImageHandler ima)

Object3DVoxels

public Object3DVoxels(ImageHandler imaSeg,
                      ImageHandler imaRaw)

Object3DVoxels

public Object3DVoxels(ImagePlus plus,
                      int val)

Deprecated. use Object3D-IJUtils Constructor for the Object3D object

Parameters:

plus - Segmented image

val - Pixel value of the object

Object3DVoxels

public Object3DVoxels(ImageStack stack,
                      int val)

Deprecated. use Object3D-IJUtils Constructor for the Object3D object

Parameters:

stack - Segmented image

val - Pixel value of the object

Object3DVoxels

public Object3DVoxels(java.util.List<Voxel3D> al)

Parameters:

al -

Object3DVoxels

public Object3DVoxels(Object3DVoxels other)

copy

Parameters:

other -

Object3DVoxels

public Object3DVoxels(Object3D other)

Method Detail

copyObject

public Object3DVoxels copyObject(int newLabel)

createSphereUnit

public void createSphereUnit(float cx,
                             float cy,
                             float cz,
                             float rad)

createEllipsoidPixel

public void createEllipsoidPixel(int cx,
                                 int cy,
                                 int cz,
                                 float rx,
                                 float ry,
                                 float rz)

addVoxelsIntersection

public void addVoxelsIntersection(Object3D ob1,
                                  Object3D ob2)

addVoxelsIntersection

public void addVoxelsIntersection(java.util.ArrayList<Object3D> objs)

addVoxelsUnion

public void addVoxelsUnion(Object3D ob1,
                           Object3D ob2)

addVoxelsUnion

public void addVoxelsUnion(java.util.ArrayList<Object3D> objs)

substractObject

public void substractObject(Object3D other)

addVoxels

public final void addVoxels(java.util.List<Voxel3D> vox)

Parameters:

vox -

removeVoxels

public void removeVoxels(int threshold)

isConnex

public boolean isConnex()

getConnexComponents

public java.util.List<Object3DVoxels> getConnexComponents()

getInterior3DFill

public Object3DVoxels getInterior3DFill()

setShowStatus

public void setShowStatus(boolean showStatus)

Parameters:

showStatus -

getPixelMax

public Voxel3D getPixelMax(ImageHandler ima)

Description copied from class: Object3D

compute the voxel with maximum value in an image

Specified by:

getPixelMax in class Object3D

Parameters:

ima - to find the maximum value

Returns:

the voxel with the max value

computeMomentsInertia

public void computeMomentsInertia()

Computation of the inertia tensor with units value

computeMoments2

protected void computeMoments2(boolean normalize)

Computation of the dispersion tensor with units value

Specified by:

computeMoments2 in class Object3D

Parameters:

normalize - normalize by volume or not

computeMoments3

public void computeMoments3()

Description copied from class: Object3D

Compute the moments of the object, order 3

Specified by:

computeMoments3 in class Object3D

computeMoments4

public void computeMoments4()

Description copied from class: Object3D

Compute the moments of the object, order 4

Specified by:

computeMoments4 in class Object3D

computeCenter

protected void computeCenter()

Compute the barycenter and the volume

Specified by:

computeCenter in class Object3D

setContours

public void setContours(java.util.LinkedList<Voxel3D> contours,
                        double areaUnit)

computeContours

public void computeContours()

Compute the contours of the object rad=0.5

Specified by:

computeContours in class Object3D

computeBounding

protected void computeBounding()

Compute the bounding box of the object

Specified by:

computeBounding in class Object3D

hasOneVoxelValueRange

public boolean hasOneVoxelValueRange(ImageHandler img,
                                     int t0,
                                     int t1)

Specified by:

hasOneVoxelValueRange in class Object3D

getVoxelInsideBoundingBox

protected java.util.List<Voxel3D> getVoxelInsideBoundingBox(int[] boundingBox)

getColoc

public int getColoc(Object3D obj)

Specified by:

getColoc in class Object3D

Returns:

hasOneVoxelColoc

public boolean hasOneVoxelColoc(Object3D obj)

Specified by:

hasOneVoxelColoc in class Object3D

Returns:

getColocVoxels

public int getColocVoxels(Object3D obj)

pcColoc2

public double pcColoc2(java.util.ArrayList<Object3DVoxels> objs)

draw

public void draw(ObjectCreator3D obj,
                 int col)

Draw the pixel inside a creator

Specified by:

draw in class Object3D

Parameters:

obj - The objectCreator to draw in

col - The value to draw

createRoi

public Roi createRoi(int z)

Deprecated. use Object3D-IJUtils Constructor for the createRoi object

Specified by:

createRoi in class Object3D

Parameters:

z - Description of the Parameter

Returns:

Description of the Return Value

draw

public boolean draw(ByteProcessor mask,
                    int z,
                    int col)

Deprecated. use Object3D-IJUtils Draw inside a particular Z

Specified by:

draw in class Object3D

Parameters:

mask - The mask image to draw

z - The Z coordinate

col - The value to draw

Returns:

drawContours

public void drawContours(ObjectCreator3D ima,
                         int col)

Parameters:

ima -

col -

drawContoursXY

public void drawContoursXY(ObjectCreator3D ima,
                           int z,
                           int col)

draw

public void draw(ImageStack mask,
                 int col)

Deprecated. use Object3D-IJUtils

Specified by:

draw in class Object3D

Parameters:

mask - the image

col - the color(grey level)

draw

public void draw(ImageStack mask,
                 int r,
                 int g,
                 int b)

Deprecated. use Object3D-IJUtils

Specified by:

draw in class Object3D

Parameters:

mask - the imagestack

r - red value

g - greeen value

b - blue value

getVoxels

public java.util.List<Voxel3D> getVoxels()

Description copied from class: Object3D

Get the list of voxels of the object

Specified by:

getVoxels in class Object3D

Returns:

the list of voxels

setVoxels

public void setVoxels(java.util.LinkedList<Voxel3D> al)

getFirstVoxel

public Voxel3D getFirstVoxel()

getRandomVoxel

public Voxel3D getRandomVoxel(java.util.Random ra)

Get a random voxel in the object

Parameters:

ra - Random Object

Returns:

next random voxel in the object

getDiscreteCompactness

public double getDiscreteCompactness()

getCompactnessCorrected

public double getCompactnessCorrected()

getSphericityCorrected

public double getSphericityCorrected()

getAreaPixelsCorrected

public double getAreaPixelsCorrected()

saveObject

public void saveObject(java.lang.String path)

Specified by:

saveObject in class Object3D

Parameters:

path -

saveObjectZip

public void saveObjectZip(java.lang.String path)

loadObject

public void loadObject(java.lang.String path,
                       java.lang.String name)

Parameters:

path -

name -

translate

public void translate(double x,
                      double y,
                      double z)

Specified by:

translate in class Object3D

translate

public void translate(Vector3D trans)

Overrides:

translate in class Object3D

rotate

public void rotate(Vector3D Axis,
                   double angle)

computeMassCenter

protected void computeMassCenter(ImageHandler ima)

Description copied from class: Object3D

Compute the mass center of the object using signal from an image

Specified by:

computeMassCenter in class Object3D

Parameters:

ima - the image with the signal intensity

computeMassCenter

protected void computeMassCenter(ImageHandler ima,
                                 ImageHandler mask)

Description copied from class: Object3D

Compute the mass center of the object using signal from an image and within a mask

Specified by:

computeMassCenter in class Object3D

Parameters:

ima - the image with the signal intensity

mask - the mask to restrain the computation

listVoxels

public java.util.List<Voxel3D> listVoxels(ImageHandler ima,
                                          double threshold)

Description copied from class: Object3D

List Voxels in the image with values > threshold

Specified by:

listVoxels in class Object3D

Parameters:

ima - The image with values

threshold - the threshold

Returns:

the list of Voxels with values > threshold

listVoxels

public java.util.List<Voxel3D> listVoxels(ImageHandler ima,
                                          double thresholdLow,
                                          double thresholdHigh)

Description copied from class: Object3D

List Voxels in the image with values > threshold0 and < threshold1

Specified by:

listVoxels in class Object3D

Parameters:

ima - The image with values

thresholdLow - the min threshold

thresholdHigh - the max threshold

Returns:

the list of Voxels with values > threshold

listVoxels

public java.util.List<java.lang.Float> listVoxels(ImageHandler ima,
                                                  int newCenterX,
                                                  int newCenterY,
                                                  int newCenterZ)

draw

public void draw(ImageHandler mask,
                 float col)

Description copied from class: Object3D

drawing inside an ImageHandler

Specified by:

draw in class Object3D

Parameters:

mask - the image

col - the real value

draw

public void draw(ImageHandler mask,
                 int col,
                 int tx,
                 int ty,
                 int tz)

Specified by:

draw in class Object3D

listValues

public ArrayUtil listValues(ImageHandler ima)

Description copied from class: Object3D

Outputs the list of Voxels values using intensity image

Specified by:

listValues in class Object3D

Parameters:

ima - the intensity image

Returns:

a array of values

listValues

public ArrayUtil listValues(ImageHandler ima,
                            float thresh)

Description copied from class: Object3D

Outputs the list of Voxels values using intensity image above a fixed threshold

Specified by:

listValues in class Object3D

Parameters:

ima - the intensity image

Returns:

a array of values

getValueArray

public float[] getValueArray(ImageHandler im)

dilate

public Object3DVoxels dilate(float dilateSize,
                             ImageInt mask,
                             int nbCPUs)

getPixMedianValue

public double getPixMedianValue(ImageHandler img)

Overrides:

getPixMedianValue in class Object3D