mcib3d.geom

Class Object3DLabel

java.lang.Object

mcib3d.geom.Object3D

mcib3d.geom.Object3DLabel

All Implemented Interfaces:

java.lang.Comparable<Object3D>

public class Object3DLabel
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 .

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
Object3DLabel(ImageInt ima, int val) constructor
Object3DLabel(ImagePlus plus, int val) Deprecated.

Method Summary

Modifier and Type	Method and Description
protected Object3DVoxels	buildObject3DVoxels()
protected void	computeBounding() Compute the bounding box of the object
protected void	computeCenter() Compute the barycenter and the volume
void	computeContours() Compute the contour voxels of the object
protected void	computeMassCenter(ImageHandler ima) compute mass center with 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
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
Roi	createRoi(int z) Deprecated.
boolean	draw(ByteProcessor mask, int z, int col) Deprecated.
void	draw(ImageHandler mask, float val) drawing inside an ImageHandler
void	draw(ImageHandler mask, int col)
void	draw(ImageHandler mask, int col, int tx, int ty, int tz)
void	draw(ImageStack mask, int col) Deprecated.
void	draw(ImageStack mask, int red, int green, int blue) Deprecated.
void	draw(ObjectCreator3D obj, int col) Draw the pixel inside a creator
void	drawIntersection(ImageStack mask, Object3DLabel other, int col) Deprecated.
void	drawIntersection(ImageStack mask, Object3DLabel other, int red, int green, int blue) Deprecated.
int	getColoc(Object3D other)
Voxel3D	getPixelMax(ImageHandler ima) compute the voxel with maximum value in an image
java.util.LinkedList<Voxel3D>	getVoxels() Get the list of voxels of the object
boolean	hasOneVoxelColoc(Object3D obj)
boolean	hasOneVoxelValueRange(ImageHandler img, int t0, int t1)
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.LinkedList	listVoxels(ImageHandler ima, double threshold) List Voxels in the image with values > threshold
java.util.LinkedList	listVoxels(ImageHandler ima, double threshold1, double threshold2) List Voxels in the image with values > threshold0 and < threshold1
void	saveObject(java.lang.String path)
void	translate(double x, double y, double z)

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, getPixMedianValue, 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, translate, 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

Object3DLabel

public Object3DLabel(ImageInt ima,
                     int val)

constructor

Parameters:

ima - Segmented image

val - Pixel value of the object

Object3DLabel

@Deprecated
public Object3DLabel(ImagePlus plus,
                                 int val)

Deprecated.

Constructor for the Object3D object

Parameters:

plus - Segmented image

val - Pixel value of the object

Method Detail

listVoxels

public java.util.LinkedList 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:

array of listed values (with coordinates)

listVoxels

public java.util.LinkedList listVoxels(ImageHandler ima,
                                       double threshold1,
                                       double threshold2)

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

threshold1 - the min threshold

threshold2 - the max threshold

Returns:

the list of Voxels with values > threshold

computeBounding

protected void computeBounding()

Compute the bounding box of the object

Specified by:

computeBounding in class Object3D

computeContours

public void computeContours()

Description copied from class: Object3D

Compute the contour voxels of the object

Specified by:

computeContours in class Object3D

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

computeCenter

protected void computeCenter()

Compute the barycenter and the volume

Specified by:

computeCenter in class Object3D

computeMassCenter

protected void computeMassCenter(ImageHandler ima)

compute mass center with an image

Specified by:

computeMassCenter in class Object3D

Parameters:

ima - the image

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

computeMoments2

public void computeMoments2(boolean normalize)

Computation of the dispersion tensor with units value

Specified by:

computeMoments2 in class Object3D

Parameters:

normalize -

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

computeMomentsInertia

public void computeMomentsInertia()

Computation of the inertia tensor with units value

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

draw

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

Deprecated.

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:

draw

public void draw(ImageHandler mask,
                 int col)

Specified by:

draw in class Object3D

Parameters:

mask -

col -

draw

public void draw(ImageHandler mask,
                 float val)

Description copied from class: Object3D

drawing inside an ImageHandler

Specified by:

draw in class Object3D

Parameters:

mask - the image

val - the real value

draw

@Deprecated
public void draw(ImageStack mask,
                             int red,
                             int green,
                             int blue)

Deprecated.

Specified by:

draw in class Object3D

Parameters:

mask -

red -

green -

blue -

draw

@Deprecated
public void draw(ImageStack mask,
                             int col)

Deprecated.

Specified by:

draw in class Object3D

Parameters:

mask -

col -

drawIntersection

@Deprecated
public void drawIntersection(ImageStack mask,
                                         Object3DLabel other,
                                         int red,
                                         int green,
                                         int blue)

Deprecated.

Parameters:

mask -

other -

red -

green -

blue -

drawIntersection

@Deprecated
public void drawIntersection(ImageStack mask,
                                         Object3DLabel other,
                                         int col)

Deprecated.

Parameters:

mask -

other -

col -

createRoi

@Deprecated
public Roi createRoi(int z)

Deprecated.

Constructor for the createRoi object

Specified by:

createRoi in class Object3D

Parameters:

z - Description of the Parameter

Returns:

Description of the Return Value

getVoxels

public java.util.LinkedList<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

buildObject3DVoxels

protected Object3DVoxels buildObject3DVoxels()

saveObject

public void saveObject(java.lang.String path)

Specified by:

saveObject in class Object3D

Parameters:

path -

translate

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

Specified by:

translate in class Object3D

getColoc

public int getColoc(Object3D other)

Specified by:

getColoc in class Object3D

Returns:

hasOneVoxelColoc

public boolean hasOneVoxelColoc(Object3D obj)

Specified by:

hasOneVoxelColoc in class Object3D

Returns:

hasOneVoxelValueRange

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

Specified by:

hasOneVoxelValueRange 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

draw

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

Specified by:

draw in class Object3D