mcib3d.geom.deformation3d

Class DeformableMesh

java.lang.Object

mcib3d.geom.Object3D

mcib3d.geom.Object3DSurface

mcib3d.geom.deformation3d.DeformableMesh

All Implemented Interfaces:

java.lang.Comparable<Object3D>

public class DeformableMesh
extends Object3DSurface

/** Copyright (C) 2008- 2012 Thomas Boudier and others This file is part of mcib3d mcib3d is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. 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.Object3DSurface

faces, faces_vertices_index, SMOOTH_BLENDER, smooth_faces, SMOOTH_IJ3D, SMOOTH_LAPLACE, vertices, vertices_faces_index, 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
DeformableMesh(java.util.List<Point3f> l)
DeformableMesh(java.util.List<Point3f> l, int val)

Method Summary

Modifier and Type	Method and Description
void	computeAllForces(boolean stats)
void	copyParameters(DeformableMesh src)
double	getAlpha()
double	getGlobalScaling()
ImageHandler	getImage()
int	getMaxDistance()
double	getOrientedScaling(Vector3D dir)
Vector3D	getRotationAxis()
double[]	getStatsForces()
double	getSumAbsForces()
double	getThresholdMax()
double	getThresholdMin()
Vector3D	getTranslation()
double	iterateGlobalScaling(double error, int nIte)
double	iterateOrientedScaling(Vector3D dir, double error, int nIte)
double	iterateRotation(Vector3D axe, double rotStep, double maxAngle)
void	iterateRoughDisplacement(double maxDispl, int maxIte)
Vector3D	iterateTranslation(double error, int nIte)
void	roughDisplacement(double maxDispl)
void	setAlpha(double alpha)
void	setImage(ImageHandler image)
void	setMaxDistance(int maxDistance)
void	setThresholdMax(double thresholdMax)
void	setThresholdMin(double thresholdMin)

Methods inherited from class mcib3d.geom.Object3DSurface

buildObject3DVoxels, computeBounding, computeCenter, computeContours, computeConvexHull3D, computeMassCenter, computeMassCenter, computeMeshSurface, computeMoments2, computeMoments3, computeMoments4, computeVerticesNormals, computeVerticesNormalsWeighted, createRoi, createSphere, deCalibrateObject, draw, draw, draw, draw, draw, draw, drawContent, drawCurvature, drawFacesCurvature, drawFacesVertex, drawMesh, drawNeighbors, drawNormal, getCenterFace, getColoc, getCurvatureFaces, getCurvatureGaussBonnet, getCurvatures, getCurvaturesGaussBonnet, getCurvatureTangent, getMeanCurvatureVertexFaces, getNbUniqueVertices, getNeighborVertices, getNormalFace, getNormalVertex, getNormalVertexWeighted, getPixelMax, getRotated, getSmoothingFactor, getSmoothSurface, getSmoothSurfaceArea, getSmoothSurfaceAreaUnit, getSurfaceMesh, getSurfaceMeshUnit, getSurfaceTriangles, getSurfaceTrianglesPixels, getSurfaceTrianglesUnit, getTangentVector, getUniqueVertex, getUniqueVerticesIndexes, getVertex, getVoxels, hasOneVoxelColoc, hasOneVoxelValueRange, invertNormals, listValues, listValues, listVoxels, listVoxels, reCalibrateObject, reCalibratePoints, rotate, saveObject, scale, scale, setSmooth_method, setSmoothingFactor, translate, translateTool

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, 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

DeformableMesh

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

DeformableMesh

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

Method Detail

getImage

public ImageHandler getImage()

setImage

public void setImage(ImageHandler image)

getAlpha

public double getAlpha()

setAlpha

public void setAlpha(double alpha)

getMaxDistance

public int getMaxDistance()

setMaxDistance

public void setMaxDistance(int maxDistance)

getThresholdMax

public double getThresholdMax()

setThresholdMax

public void setThresholdMax(double thresholdMax)

getThresholdMin

public double getThresholdMin()

setThresholdMin

public void setThresholdMin(double thresholdMin)

copyParameters

public void copyParameters(DeformableMesh src)

computeAllForces

public void computeAllForces(boolean stats)

getSumAbsForces

public double getSumAbsForces()

getStatsForces

public double[] getStatsForces()

getTranslation

public Vector3D getTranslation()

iterateTranslation

public Vector3D iterateTranslation(double error,
                                   int nIte)

getGlobalScaling

public double getGlobalScaling()

iterateGlobalScaling

public double iterateGlobalScaling(double error,
                                   int nIte)

getOrientedScaling

public double getOrientedScaling(Vector3D dir)

iterateOrientedScaling

public double iterateOrientedScaling(Vector3D dir,
                                     double error,
                                     int nIte)

getRotationAxis

public Vector3D getRotationAxis()

iterateRotation

public double iterateRotation(Vector3D axe,
                              double rotStep,
                              double maxAngle)

roughDisplacement

public void roughDisplacement(double maxDispl)

iterateRoughDisplacement

public void iterateRoughDisplacement(double maxDispl,
                                     int maxIte)