public class Object3DFuzzy extends Object3DVoxels
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 and Description |
|---|
Object3DFuzzy(int label,
java.util.LinkedList<Voxel3D> voxels) |
| Modifier and Type | Method and Description |
|---|---|
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
|
void |
computeMoments2(boolean normalize)
Computation of the dispersion tensor with units value
|
Roi |
createRoi(int z) |
boolean |
draw(ByteProcessor mask,
int z,
int col) |
void |
draw(ImageStack mask,
int col) |
void |
draw(ImageStack mask,
int r,
int g,
int b) |
void |
drawContours(ObjectCreator3D ima,
int col) |
java.util.LinkedList<Voxel3D> |
getContours()
return the list of contour voxels
|
Voxel3D |
getPixelMax(ImageHandler ima)
compute the voxel with maximum value in an image
|
Voxel3D |
getPixelMin(ImageHandler ima) |
java.util.LinkedList<Voxel3D> |
getVoxels()
Get the list of voxels of the object
|
java.util.LinkedList |
listVoxels(ImageHandler ima)
gets the list of all pixels within an image as an ArrayList
|
void |
saveObject(java.lang.String path) |
void |
setContours(java.util.LinkedList<Voxel3D> contours) |
addVoxels, addVoxelsIntersection, addVoxelsIntersection, addVoxelsUnion, addVoxelsUnion, computeMassCenter, computeMoments3, computeMoments4, computeMomentsInertia, copyObject, createEllipsoidPixel, createSphereUnit, dilate, draw, draw, drawContoursXY, getAreaPixelsCorrected, getColoc, getColocVoxels, getCompactnessCorrected, getConnexComponents, getDiscreteCompactness, getFirstVoxel, getInterior3DFill, getPixMedianValue, getRandomvoxel, getRandomVoxel, getSphericityCorrected, getValueArray, getVoxelInsideBoundingBox, hasOneVoxelColoc, hasOneVoxelValueRange, isConnex, listValues, listValues, listVoxels, listVoxels, listVoxels, loadObject, pcColoc2, removeVoxels, rotate, setContours, setShowStatus, setVoxels, substractObject, translate, translateangle, 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, 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, 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, VoxelsBorderBorderpublic Object3DFuzzy(int label,
java.util.LinkedList<Voxel3D> voxels)
public java.util.LinkedList<Voxel3D> getContours()
Object3DgetContours in class Object3Dpublic void setContours(java.util.LinkedList<Voxel3D> contours)
protected void computeCenter()
Object3DVoxelscomputeCenter in class Object3DVoxelsprotected void computeMassCenter(ImageHandler ima)
Object3DcomputeMassCenter in class Object3DVoxelsima - the image with the signal intensityprotected void computeBounding()
Object3DVoxelscomputeBounding in class Object3DVoxelspublic void computeContours()
Object3DVoxelscomputeContours in class Object3DVoxelspublic void computeMoments2(boolean normalize)
Object3DVoxelscomputeMoments2 in class Object3DVoxelsnormalize - normalize by volume or notpublic Voxel3D getPixelMax(ImageHandler ima)
Object3DgetPixelMax in class Object3DVoxelsima - to find the maximum valuepublic Voxel3D getPixelMin(ImageHandler ima)
public java.util.LinkedList listVoxels(ImageHandler ima)
Object3DlistVoxels in class Object3Dima - the image with signalpublic void drawContours(ObjectCreator3D ima, int col)
drawContours in class Object3DVoxelspublic void draw(ImageStack mask,
int col)
draw in class Object3DVoxelsmask - the imagecol - the color(grey level)public void draw(ImageStack mask,
int r,
int g,
int b)
draw in class Object3DVoxelsmask - the imagestackr - red valueg - greeen valueb - blue valuepublic boolean draw(ByteProcessor mask,
int z,
int col)
draw in class Object3DVoxelsmask - The mask image to drawz - The Z coordinatecol - The value to drawpublic Roi createRoi(int z)
createRoi in class Object3DVoxelsz - Description of the Parameterpublic java.util.LinkedList<Voxel3D> getVoxels()
Object3DgetVoxels in class Object3DVoxelspublic void saveObject(java.lang.String path)
saveObject in class Object3DVoxels