mcib3d.geom

Class Object3DSurface

java.lang.Object

mcib3d.geom.Object3D

mcib3d.geom.Object3DSurface

All Implemented Interfaces:

java.lang.Comparable<Object3D>

Direct Known Subclasses:

DeformableMesh

public class Object3DSurface
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

Modifier and Type	Field and Description
protected java.util.List<Point3f>	faces
protected java.util.List<java.lang.Integer>	faces_vertices_index
static int	SMOOTH_BLENDER
protected java.util.List<Point3f>	smooth_faces
static int	SMOOTH_IJ3D
static int	SMOOTH_LAPLACE
protected java.util.List<Point3f>	vertices
protected java.util.List<java.util.List<java.lang.Integer>>	vertices_faces_index
protected java.util.ArrayList<Vector3D>	verticesNormals

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
Object3DSurface(java.util.List<Point3f> l)
Object3DSurface(java.util.List<Point3f> l, int val)

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 of the object
void	computeContours() Compute the contour voxels of the object
java.util.LinkedList<Point3f>	computeConvexHull3D()
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
java.util.List	computeMeshSurface(boolean calibrated) Deprecated.
protected void	computeMoments2(boolean normalize) Compute the moments of the object (for ellipsoid orientation), order 2
protected void	computeMoments3() Compute the moments of the object, order 3
void	computeMoments4() Compute the moments of the object, order 4
void	computeVerticesNormals()
void	computeVerticesNormalsWeighted()
Roi	createRoi(int z) Deprecated.
static java.util.List<Point3f>	createSphere(GeomTransform3D transform, int meridians, int parallels)
void	deCalibrateObject()
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, int tx, int ty, int tz)
void	draw(ImageStack mask, int col) Deprecated.
void	draw(ImageStack mask, int r, int g, int b) Deprecated.
void	draw(ObjectCreator3D obj, int col)
Content	drawContent(Image3DUniverse univ, Color3f co, java.lang.String name)
void	drawCurvature(ImageFloat draw, double[] curvatures)
Content	drawFacesCurvature(Image3DUniverse univ, double[] cur, java.lang.String name, boolean useCalibration)
Content	drawFacesVertex(int i, Image3DUniverse univ, Color3f co, java.lang.String name, boolean useCalibration)
void	drawMesh(ObjectCreator3D obj, int col)
Content	drawNeighbors(int v, Image3DUniverse univ, Color3f co, java.lang.String name, boolean useCalibration)
Content	drawNormal(int i, double le, Image3DUniverse univ, Color3f co, java.lang.String name, boolean useCalibration)
Point3f	getCenterFace(int idx)
int	getColoc(Object3D obj)
double[]	getCurvatureFaces(double[] curvatures)
double	getCurvatureGaussBonnet(int ve)
double[]	getCurvatures(int v)
double[]	getCurvaturesGaussBonnet()
double	getCurvatureTangent(int v0, int v1)
double[]	getMeanCurvatureVertexFaces(double[] facesCurvatures)
int	getNbUniqueVertices()
java.util.ArrayList<java.lang.Integer>	getNeighborVertices(int v)
Point3f	getNormalFace(int idx)
Point3f	getNormalVertex(int idx)
Point3f	getNormalVertexWeighted(int idx)
Voxel3D	getPixelMax(ImageHandler ima) compute the voxel with maximum value in an image
java.util.ArrayList<Point3f>	getRotated(Vector3D Axis, double angle)
float	getSmoothingFactor()
java.util.List<Point3f>	getSmoothSurface()
double	getSmoothSurfaceArea()
double	getSmoothSurfaceAreaUnit()
double	getSurfaceMesh()
double	getSurfaceMeshUnit()
java.util.List<Point3f>	getSurfaceTriangles(boolean calibrated)
java.util.List<Point3f>	getSurfaceTrianglesPixels(boolean smooth)
java.util.List<Point3f>	getSurfaceTrianglesUnit(boolean smooth)
Point3f	getTangentVector(int v0, int v1)
Point3f	getUniqueVertex(int i)
java.util.List<java.util.List<java.lang.Integer>>	getUniqueVerticesIndexes()
Point3f	getVertex(int i)
java.util.LinkedList<Voxel3D>	getVoxels() Get the list of voxels of the object
boolean	hasOneVoxelColoc(Object3D obj)
boolean	hasOneVoxelValueRange(ImageHandler ima, int t0, int t1)
static java.util.List<Point3f>	invertNormals(java.util.List<Point3f> li)
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	reCalibrateObject()
void	reCalibratePoints()
void	rotate(Vector3D Axis, double angle)
void	saveObject(java.lang.String path)
void	scale(double scale)
void	scale(double scale, Vector3D dir)
void	setSmooth_method(int method)
void	setSmoothingFactor(float fac)
void	translate(double x, double y, double z)
static java.util.List	translateTool(java.util.List l, float tx, float ty, float tz)

Methods inherited from class mcib3d.geom.Object3D

angle, b_closed, b_open, centerInside, compareTo, computeContours, computeEigen, createIntersectionImage, createIntersectionImage, createSegImage, createSegImage, createSegImageMini2D, disjointBox, distBorderPixel, distBorderUnit, distBorderUnit, distCenter2DUnit, distCenterBorderUnit, 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, getDistCenterMean, getDistCenterMin, getDistCenterSigma, 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

Field Detail

SMOOTH_LAPLACE

public static final int SMOOTH_LAPLACE

See Also:

Constant Field Values

SMOOTH_IJ3D

public static final int SMOOTH_IJ3D

See Also:

Constant Field Values

SMOOTH_BLENDER

public static final int SMOOTH_BLENDER

See Also:

Constant Field Values

faces

protected java.util.List<Point3f> faces

smooth_faces

protected java.util.List<Point3f> smooth_faces

vertices

protected java.util.List<Point3f> vertices

vertices_faces_index

protected java.util.List<java.util.List<java.lang.Integer>> vertices_faces_index

faces_vertices_index

protected java.util.List<java.lang.Integer> faces_vertices_index

verticesNormals

protected java.util.ArrayList<Vector3D> verticesNormals

Constructor Detail

Object3DSurface

public Object3DSurface(java.util.List<Point3f> l)

Parameters:

l -

Object3DSurface

public Object3DSurface(java.util.List<Point3f> l,
                       int val)

Parameters:

l -

val -

Method Detail

invertNormals

public static java.util.List<Point3f> invertNormals(java.util.List<Point3f> li)

createSphere

public static java.util.List<Point3f> createSphere(GeomTransform3D transform,
                                                   int meridians,
                                                   int parallels)

Parameters:

transform -

meridians -

parallels -

Returns:

translateTool

public static java.util.List translateTool(java.util.List l,
                                           float tx,
                                           float ty,
                                           float tz)

deCalibrateObject

public void deCalibrateObject()

reCalibrateObject

public void reCalibrateObject()

reCalibratePoints

public void reCalibratePoints()

getSmoothSurfaceArea

public double getSmoothSurfaceArea()

Returns:

getSmoothSurfaceAreaUnit

public double getSmoothSurfaceAreaUnit()

Returns:

getSurfaceMesh

public double getSurfaceMesh()

Returns:

getSurfaceMeshUnit

public double getSurfaceMeshUnit()

Returns:

getSmoothSurface

public java.util.List<Point3f> getSmoothSurface()

Returns:

getSurfaceTrianglesPixels

public java.util.List<Point3f> getSurfaceTrianglesPixels(boolean smooth)

Parameters:

smooth -

Returns:

getSurfaceTrianglesUnit

public java.util.List<Point3f> getSurfaceTrianglesUnit(boolean smooth)

computeConvexHull3D

public java.util.LinkedList<Point3f> computeConvexHull3D()

getSmoothingFactor

public float getSmoothingFactor()

Returns:

setSmoothingFactor

public void setSmoothingFactor(float fac)

Parameters:

fac -

setSmooth_method

public void setSmooth_method(int method)

Parameters:

method -

getNormalFace

public Point3f getNormalFace(int idx)

getCenterFace

public Point3f getCenterFace(int idx)

getNormalVertex

public Point3f getNormalVertex(int idx)

getNormalVertexWeighted

public Point3f getNormalVertexWeighted(int idx)

computeVerticesNormals

public void computeVerticesNormals()

computeVerticesNormalsWeighted

public void computeVerticesNormalsWeighted()

getTangentVector

public Point3f getTangentVector(int v0,
                                int v1)

getCurvatureTangent

public double getCurvatureTangent(int v0,
                                  int v1)

getCurvatureGaussBonnet

public double getCurvatureGaussBonnet(int ve)

getCurvatureFaces

public double[] getCurvatureFaces(double[] curvatures)

getMeanCurvatureVertexFaces

public double[] getMeanCurvatureVertexFaces(double[] facesCurvatures)

getCurvaturesGaussBonnet

public double[] getCurvaturesGaussBonnet()

getCurvatures

public double[] getCurvatures(int v)

drawCurvature

public void drawCurvature(ImageFloat draw,
                          double[] curvatures)

getNeighborVertices

public java.util.ArrayList<java.lang.Integer> getNeighborVertices(int v)

computeCenter

protected void computeCenter()

Description copied from class: Object3D

Compute the barycenter of the object

Specified by:

computeCenter in class Object3D

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

computeBounding

protected void computeBounding()

Description copied from class: Object3D

Compute the bounding box of the object

Specified by:

computeBounding in class Object3D

getUniqueVerticesIndexes

public java.util.List<java.util.List<java.lang.Integer>> getUniqueVerticesIndexes()

computeContours

public void computeContours()

Description copied from class: Object3D

Compute the contour voxels of the object

Specified by:

computeContours in class Object3D

computeMoments2

protected void computeMoments2(boolean normalize)

Description copied from class: Object3D

Compute the moments of the object (for ellipsoid orientation), order 2

Specified by:

computeMoments2 in class Object3D

Parameters:

normalize - normalize by volume or not

computeMoments3

protected 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

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 - the image

Returns:

the max voxel

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:

the list of Voxels with values > threshold

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

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()

getVertex

public Point3f getVertex(int i)

getUniqueVertex

public Point3f getUniqueVertex(int i)

getNbUniqueVertices

public int getNbUniqueVertices()

getSurfaceTriangles

public java.util.List<Point3f> getSurfaceTriangles(boolean calibrated)

Parameters:

calibrated -

Returns:

computeMeshSurface

@Deprecated
public java.util.List computeMeshSurface(boolean calibrated)

Deprecated.

Overrides:

computeMeshSurface in class Object3D

Returns:

drawMesh

public void drawMesh(ObjectCreator3D obj,
                     int col)

draw

public void draw(ObjectCreator3D obj,
                 int col)

Specified by:

draw in class Object3D

Parameters:

obj - the image

col - the color(grey level)

draw

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

Deprecated.

Specified by:

draw in class Object3D

Parameters:

mask - the byte processor

z - the z slice

col - the color(grey level)

Returns:

draw

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

Deprecated.

Specified by:

draw in class Object3D

Parameters:

mask - the image

col - the color(grey level)

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

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

Specified by:

draw in class Object3D

drawContent

public Content drawContent(Image3DUniverse univ,
                           Color3f co,
                           java.lang.String name)

drawNormal

public Content drawNormal(int i,
                          double le,
                          Image3DUniverse univ,
                          Color3f co,
                          java.lang.String name,
                          boolean useCalibration)

drawFacesVertex

public Content drawFacesVertex(int i,
                               Image3DUniverse univ,
                               Color3f co,
                               java.lang.String name,
                               boolean useCalibration)

drawFacesCurvature

public Content drawFacesCurvature(Image3DUniverse univ,
                                  double[] cur,
                                  java.lang.String name,
                                  boolean useCalibration)

drawNeighbors

public Content drawNeighbors(int v,
                             Image3DUniverse univ,
                             Color3f co,
                             java.lang.String name,
                             boolean useCalibration)

draw

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

Deprecated.

Specified by:

draw in class Object3D

Parameters:

mask - the imagestack

r - red value

g - greeen value

b - blue value

createRoi

@Deprecated
public Roi createRoi(int z)

Deprecated.

Specified by:

createRoi in class Object3D

Parameters:

z - the z slice

Returns:

the contour roi in slice z

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

scale

public void scale(double scale)

scale

public void scale(double scale,
                  Vector3D dir)

rotate

public void rotate(Vector3D Axis,
                   double angle)

getRotated

public java.util.ArrayList<Point3f> getRotated(Vector3D Axis,
                                               double angle)

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:

hasOneVoxelValueRange

public boolean hasOneVoxelValueRange(ImageHandler ima,
                                     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