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java.lang.Object ij3d.geom.Object3D
public class Object3D
An Object3D in an image
Field Summary | |
---|---|
protected int |
area
Area |
protected double |
bx
IsoBarycenter |
protected double |
by
|
protected double |
bz
|
protected Pixel3D[] |
contours
Contours pixels |
protected double |
cx
Center of mass |
protected double |
cy
|
protected double |
cz
|
protected EigenvalueDecomposition |
eigen
Matrix of decomposition |
protected double |
feret
feret diameter |
protected Pixel3D |
feret1
|
protected Pixel3D |
feret2
|
protected double |
integratedDensity
Integrated density (sum of pixels) |
protected double |
pixmax
Max pix value in object |
protected double |
pixmin
Min pix value in object |
protected IntImage3D |
segImage
The image where the object lies |
protected double |
sigma
|
protected double |
sxx
Centred Moments |
protected double |
sxy
Centred Moments |
protected double |
sxz
Centred Moments |
protected double |
syy
Centred Moments |
protected double |
syz
Centred Moments |
protected double |
szz
Centred Moments |
protected boolean |
touchBorders
Touch the borders ? |
protected int |
value
Value (grey-level) |
protected int |
volume
volume |
protected int |
xmax
Bounding box |
protected int |
xmin
Bounding box |
protected int |
ymax
Bounding box |
protected int |
ymin
Bounding box |
protected int |
zmax
Bounding box |
protected int |
zmin
Bounding box |
Constructor Summary | |
---|---|
Object3D(ij.ImagePlus plus,
int val)
Constructor for the Object3D object |
|
Object3D(IntImage3D ima,
int val)
constructeur |
|
Object3D(Object3D other)
|
Method Summary | |
---|---|
double |
angle(Object3D a,
Object3D b)
Angle between (a, this, b) with real coordinates |
void |
computeBounding()
Compute the bounding box of the object |
void |
computeCenter()
Compute the barycenter and the volume |
void |
computeContours()
Compute the contours of the object rad=0.5 |
void |
computeContours(IntImage3D ima)
|
void |
computeMassCenter(Image3D ima)
compute mass center with an image |
void |
computeMoments()
Computation of the dispersion tensor with units value |
void |
computeMomentsInertia()
Computation of the inertia tensor with units value |
ij.gui.Roi |
createRoi(int z)
Constructor for the createRoi object |
double |
distBorder(Object3D autre)
the minimum distance between two objets (in real distance) computed on the contours pixels |
double |
distCenter(Object3D autre)
distance from center to center (in real distance) |
double |
distCenter2D(Object3D autre)
2D distance from center to center (in real distance) |
double |
distCenterBorder(Object3D autre)
Distance center to the border |
double |
distPixelBorder(double x,
double y,
double z)
Distance from a point to the border of the object |
double |
distPixelBorder(double x,
double y,
double z,
Vector3D V)
Distance from a point along a direction to the border of the object |
double |
distPixelBorder(Point3D P)
|
double |
distPixelCenter(double x,
double y,
double z)
|
void |
draw(ij.process.ByteProcessor mask,
int z,
int col)
Description of the Method |
void |
draw(ij.ImageStack mask,
int col)
|
void |
draw(ij.ImageStack mask,
int red,
int green,
int blue)
|
void |
draw(IntImage3D mask,
int col)
|
void |
draw(ObjectCreator3D obj,
int col)
Description of the Method |
void |
drawContours(ObjectCreator3D ima,
int col)
|
void |
drawIntersection(ij.ImageStack mask,
Object3D other,
int col)
|
void |
drawIntersection(ij.ImageStack mask,
Object3D other,
int red,
int green,
int blue)
|
int |
getAreaPixels()
the area of the Object3D (in pixels) |
double |
getAreaUnit()
Gets the areaUnit attribute of the Object3D object |
ij.measure.Calibration |
getCalibration()
Gets the calibration attribute of the Object3D object |
Vector3D |
getCenter()
Gets the center attribute of the Object3D object |
Vector3D |
getCenterUnit()
Gets the centerUnit attribute of the Object3D object |
double |
getCenterX()
x coordinate of the center |
double |
getCenterY()
y coordinate of the center |
double |
getCenterZ()
z coordinate of the center |
double |
getCompacite()
Gets the compacite attribute of the Object3D (unit) |
double |
getDistCenterMax()
|
double |
getDistCenterMean()
|
double |
getDistCenterMin()
|
double |
getDistCenterSigma()
|
double |
getFeret()
Gets the feret attribute of the Object3D object (unit) |
Pixel3D |
getFeretPixel1()
|
Pixel3D |
getFeretPixel2()
|
double |
getIntegratedDensity(Image3D ima)
integrated density of the Object3D |
Vector3D |
getMainAxis()
Gets the mainAxis attribute of the Object3D object (unit) |
double |
getMainElongationAxis()
Gets the elongationAxis attribute of the Object3D object (unit) |
double |
getMassCenterX(Image3D ima)
x coordinate of the center |
double |
getMassCenterY(Image3D ima)
y coordinate of the center |
double |
getMassCenterZ(Image3D ima)
z coordinate of the center |
Matrix |
getMatrixAxes()
Gets the main axes vectors as a matrix |
double |
getMeanPixValue(Image3D ima)
Gets the meanPixValue attribute of the Object3D object |
double |
getMedianElongationAxis()
Gets the elongationAxis attribute of the Object3D object (unit) |
Pixel3D |
getPixelMax(Image3D ima)
|
double |
getPixMaxValue(Image3D ima)
Gets the pixMaxValue attribute of the Object3D object |
double |
getPixMinValue(Image3D ima)
Gets the pixMinValue attribute of the Object3D object |
double |
getRatioBox()
Gets the ration between volume and volume of the bounding box (in units) |
double |
getResXY()
Gets the resXY attribute of the Object3D object |
double |
getResZ()
Gets the resZ attribute of the Object3D object |
IntImage3D |
getSegImage()
Gets the segImage attribute of the Object3D object |
double |
getSigmaPixValue(Image3D ima)
Gets the sigmaPixValue attribute of the Object3D object |
boolean |
getTouchBorders()
Gets the touchBorders attribute of the FishObject3D Object3D |
java.lang.String |
getUnits()
Gets the unit attribute of the Object3D object |
int |
getValue()
value of the Object3D (in gray level) |
double |
getValueAxis(int order)
Gets the valueAxis attribute of the Object3D object (unit) |
Vector3D |
getVectorAxis(int order)
Gets the Axis attribute of the Object3D object (unit) |
int |
getVolumePixels()
volume of the Object3D (in pixel) |
double |
getVolumeUnit()
Gets the volumeUnit attribute of the Object3D object |
int |
getXmax()
Gets the xmax attribute of the Object3D |
int |
getXmin()
Gets the xmin attribute of the Object3D |
int |
getYmax()
Gets the ymax attribute of the Object3D |
int |
getYmin()
Gets the ymin attribute of the Object3D |
int |
getZmax()
Gets the zmax attribute of the Object3D |
int |
getZmin()
Gets the zmin attribute of the Object3D |
boolean |
insideBounding(double x,
double y,
double z)
test if the point is inside the bounding box of the object |
boolean |
insideBounding(float x,
float y,
float z)
test if the point is inside the bounding box of the object |
boolean |
intersectionBox(Object3D autre)
Test if the bouding boxes intersect |
protected boolean |
isContour(int x,
int y,
int z)
the pixel is in the contour |
java.util.ArrayList |
listVoxels(Image3D ima)
|
double |
pcColoc(Object3D other)
|
double |
pixelsContact(Object3D other,
double dist_max)
|
double |
radiusCenter(Object3D obj)
|
double |
radiusCenter(Vector3D V)
|
double |
radiusPixel(double x,
double y,
double z)
|
boolean |
segmentSpot(int xdep,
int ydep,
int zdep,
int seuil,
int val,
IntImage3D originalImage)
Segment an object from a seed |
boolean |
segmentSpotMax(int xdep,
int ydep,
int zdep,
int seuil,
int val,
IntImage3D originalImage)
Segment an object from a seed, keep only max local |
boolean |
separeSpot2D(IntImage3D ori,
int val,
int seuil,
Object3D f,
Object3D f1,
Object3D f2,
double dist,
int p1,
int p2)
|
void |
setCalibration(ij.measure.Calibration cal)
Sets the calibration attribute of the Object3D object |
void |
setResolution(double rxy,
double rz,
java.lang.String u)
Sets the resolution attribute of the ObjectCreator3D object |
void |
setResXY(double rxy)
Sets the resXY attribute of the Object3D object |
void |
setResZ(double rz)
Sets the resZ attribute of the Object3D object |
void |
setUnits(java.lang.String u)
Sets the units attribute of the Object3D object |
void |
setValue(int v)
Sets the value attribute of the Object3D object |
java.lang.String |
toString()
Display information |
Vector3D |
vectorBorderBorder(Object3D autre)
The vector between the two closest border to border point |
Vector3D |
vectorCenterBorder(Object3D autre)
The vector between the center and border point |
Vector3D |
vectorPixelBorder(double x,
double y,
double z)
Vector between a pixel and the closest border |
Vector3D |
vectorPixelBorder(double x,
double y,
double z,
Vector3D V)
Vector from a point along a direction to the border of the object |
Vector3D |
vectorPixelBorder(Vector3D V)
Vector between a pixel and the closest border |
Vector3D |
vectorPixelUnitBorder(double x,
double y,
double z)
Description of the Method |
Vector3D |
vectorPixelUnitBorder(double x,
double y,
double z,
Vector3D dir)
Description of the Method |
Vector3D |
vectorPixelUnitBorder(Vector3D V)
Description of the Method |
Vector3D |
vectorPixelUnitBorder(Vector3D V,
Vector3D dir)
Description of the Method |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected int xmin
protected int ymin
protected int zmin
protected int xmax
protected int ymax
protected int zmax
protected double bx
protected double by
protected double bz
protected double cx
protected double cy
protected double cz
protected int area
protected int volume
protected double feret
protected Pixel3D feret1
protected Pixel3D feret2
protected double integratedDensity
protected double sigma
protected double pixmin
protected double pixmax
protected int value
protected Pixel3D[] contours
protected boolean touchBorders
protected double sxx
protected double sxy
protected double sxz
protected double syy
protected double syz
protected double szz
protected EigenvalueDecomposition eigen
protected IntImage3D segImage
Constructor Detail |
---|
public Object3D(IntImage3D ima, int val)
ima
- Segmented iamgeval
- Pixel value of the objectpublic Object3D(ij.ImagePlus plus, int val)
plus
- Segmented imageval
- Pixel value of the objectpublic Object3D(Object3D other)
other
- Method Detail |
---|
public void setResXY(double rxy)
rxy
- The new resXY valuepublic void setResZ(double rz)
rz
- The new resZ valuepublic void setUnits(java.lang.String u)
u
- The new units valuepublic double getResXY()
public double getResZ()
public java.lang.String getUnits()
public ij.measure.Calibration getCalibration()
public void setCalibration(ij.measure.Calibration cal)
cal
- The new calibration valuepublic final void setResolution(double rxy, double rz, java.lang.String u)
rxy
- The new resolution in XYrz
- The new resolution in Zu
- The new resolution unitprotected boolean isContour(int x, int y, int z)
x
- x coordinatey
- y coordinatez
- z coordinate
public int getVolumePixels()
public double getVolumeUnit()
public double getIntegratedDensity(Image3D ima)
ima
-
public double getCompacite()
public double getRatioBox()
public double getFeret()
public Pixel3D getFeretPixel1()
public Pixel3D getFeretPixel2()
public double getDistCenterMin()
public double getDistCenterMax()
public double getDistCenterMean()
public double getDistCenterSigma()
public int getAreaPixels()
public double getAreaUnit()
public Vector3D getCenter()
public Vector3D getCenterUnit()
public double getCenterX()
public double getCenterY()
public double getCenterZ()
public double getMassCenterX(Image3D ima)
ima
-
public double getMassCenterY(Image3D ima)
ima
-
public double getMassCenterZ(Image3D ima)
ima
-
public double getMeanPixValue(Image3D ima)
ima
-
public double getSigmaPixValue(Image3D ima)
ima
-
public double getPixMinValue(Image3D ima)
ima
-
public double getPixMaxValue(Image3D ima)
ima
-
public Pixel3D getPixelMax(Image3D ima)
ima
-
public int getXmin()
public int getYmin()
public int getZmin()
public int getXmax()
public int getYmax()
public int getZmax()
public int getValue()
public void setValue(int v)
v
- The new value valuepublic IntImage3D getSegImage()
public boolean getTouchBorders()
public double distCenter2D(Object3D autre)
autre
- the other Object3D
public double distCenter(Object3D autre)
autre
- the other Object3D (has the same resolution !)
public double angle(Object3D a, Object3D b)
a
- Object3D ab
- Object3D b
public double distBorder(Object3D autre)
autre
- the other Object3D
public Vector3D vectorBorderBorder(Object3D autre)
autre
- the othe object
public Vector3D vectorCenterBorder(Object3D autre)
autre
- the othe object
public double distCenterBorder(Object3D autre)
autre
- Other object
public double distPixelBorder(double x, double y, double z)
x
- x coordinate of the pointy
- y coordinate of the pointz
- z coordinate of the point
public double distPixelCenter(double x, double y, double z)
x
- y
- z
-
public double distPixelBorder(Point3D P)
P
-
public Vector3D vectorPixelUnitBorder(double x, double y, double z)
x
- Description of the Parametery
- Description of the Parameterz
- Description of the Parameter
public Vector3D vectorPixelUnitBorder(double x, double y, double z, Vector3D dir)
x
- Description of the Parametery
- Description of the Parameterz
- Description of the Parameterdir
- Description of the Parameter
public Vector3D vectorPixelBorder(double x, double y, double z)
x
- x coordinate of the pixely
- y coordinate of the pixelz
- z coordinate of the pixel
public Vector3D vectorPixelBorder(Vector3D V)
V
- Description of the Parameter
public Vector3D vectorPixelUnitBorder(Vector3D V)
V
- Description of the Parameter
public Vector3D vectorPixelUnitBorder(Vector3D V, Vector3D dir)
V
- Description of the Parameterdir
- Description of the Parameter
public double distPixelBorder(double x, double y, double z, Vector3D V)
x
- x coordinate of the pointy
- y coordinate of the pointz
- z coordinate of the pointV
- the direction vector
public double radiusPixel(double x, double y, double z)
x
- y
- z
-
public double radiusCenter(Vector3D V)
V
-
public double radiusCenter(Object3D obj)
obj
-
public Vector3D vectorPixelBorder(double x, double y, double z, Vector3D V)
x
- x coordinate of the pointy
- y coordinate of the pointz
- z coordinate of the pointV
- the direction vector
public boolean insideBounding(float x, float y, float z)
x
- x coordinate of the pointy
- y coordinate of the pointz
- z coordinate of the point
public boolean insideBounding(double x, double y, double z)
x
- x coordinate of the pointy
- y coordinate of the pointz
- z coordinate of the point
public boolean intersectionBox(Object3D autre)
autre
- the othe object
public double pcColoc(Object3D other)
other
- object
public java.util.ArrayList listVoxels(Image3D ima)
ima
-
public double pixelsContact(Object3D other, double dist_max)
other
- objectdist_max
- in pixel betwenn two contour points
public void computeMomentsInertia()
public void computeMoments()
public void computeMassCenter(Image3D ima)
ima
- the imagepublic final void computeCenter()
public void computeContours()
public void computeContours(IntImage3D ima)
ima
- public final void computeBounding()
public Matrix getMatrixAxes()
public Vector3D getVectorAxis(int order)
order
- the order of the axis
public double getValueAxis(int order)
order
- the order of the value
public Vector3D getMainAxis()
public double getMainElongationAxis()
public double getMedianElongationAxis()
public boolean segmentSpot(int xdep, int ydep, int zdep, int seuil, int val, IntImage3D originalImage)
seuil
- Threshold to connect pixelsval
- value of the objectxdep
- x coordinate of the seedydep
- y coordinate of the seedzdep
- z coordinate of the seedoriginalImage
- original image with the values
public boolean segmentSpotMax(int xdep, int ydep, int zdep, int seuil, int val, IntImage3D originalImage)
seuil
- Threshold to connect pixelsval
- value of the objectxdep
- x coordinate of the seedydep
- y coordinate of the seedzdep
- z coordinate of the seedoriginalImage
- original image with the values
public void draw(ObjectCreator3D obj, int col)
obj
- Description of the Parametercol
- Description of the Parameterpublic ij.gui.Roi createRoi(int z)
z
- Description of the Parameter
public void draw(ij.process.ByteProcessor mask, int z, int col)
mask
- Description of the Parameterz
- Description of the Parametercol
- Description of the Parameterpublic void draw(IntImage3D mask, int col)
mask
- col
- public void drawContours(ObjectCreator3D ima, int col)
ima
- col
- public void draw(ij.ImageStack mask, int red, int green, int blue)
mask
- red
- green
- blue
- public void drawIntersection(ij.ImageStack mask, Object3D other, int red, int green, int blue)
mask
- other
- red
- green
- blue
- public void draw(ij.ImageStack mask, int col)
mask
- col
- public void drawIntersection(ij.ImageStack mask, Object3D other, int col)
mask
- other
- col
- public boolean separeSpot2D(IntImage3D ori, int val, int seuil, Object3D f, Object3D f1, Object3D f2, double dist, int p1, int p2)
ori
- val
- seuil
- f
- f1
- f2
- dist
- p1
- p2
-
public java.lang.String toString()
toString
in class java.lang.Object
|
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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |