ij3d.image3d
Class Image3D

java.lang.Object
  extended by ij3d.image3d.Image3D
Direct Known Subclasses:
IntImage3D, RealImage3D

public abstract class Image3D
extends java.lang.Object

Description of the Class

Author:
cedric

Field Summary
static int BYTE
          Description of the Field
protected  float centerx
          Description of the Field
protected  float centery
          Description of the Field
protected  float centerz
          Description of the Field
static int FLOAT
          Description of the Field
protected  Pixel3D max
          Description of the Field
protected  float mean
          Description of the Field
protected  Pixel3D min
          Description of the Field
static int SHORT
          Description of the Field
protected  float sigma
          Description of the Field
protected  int sizex
          Description of the Field
protected  int sizey
          Description of the Field
protected  int sizez
          Description of the Field
protected  ij.ImageStack stack
          Description of the Field
 int type
          Description of the Field
static int XAXIS
          Description of the Field
static int YAXIS
          Description of the Field
static int ZAXIS
          Description of the Field
 
Constructor Summary
Image3D(ij.ImageStack pile)
          Constructor for the Image3D object
Image3D(int sizex, int sizey, int sizez, int type)
          Constructor for the Image3D object
 
Method Summary
abstract  IntImage3D binarisation(int seuilb, int seuilh)
          binarisation de l'image, creation d'une image avec 255 si entre les deux seuils
 void computeMinMax()
          Description of the Method
 int[] createKernelEllipsoid(float radx, float rady, float radz)
           
abstract  Image3D createLocalMaximaImage(int voisx, int voisy, int voisz, boolean keep)
          Création d'une image des maxima locaux dans un voisinage donne
 Image3D crop(int newzerox, int newzeroy, int newzeroz, int newsizex, int newsizey, int newsizez)
          Description of the Method
 Image3D extract(int x0, int y0, int z0, int rx, int ry, int rz, boolean sphere)
          extract a 3D image from a specified location as the center of crop
 float getCenterX()
          Gets the centerX attribute of the Image3D object
 float getCenterY()
          Gets the centerY attribute of the Image3D object
 float getCenterZ()
          Gets the centerZ attribute of the Image3D object
protected  double getFloatMaximum()
          Gets the floatMaximum attribute of the Image3D object
protected  double getFloatMinimum()
          Gets the floatMinimum attribute of the Image3D object
abstract  TabUtil getHistogram()
          donne l'histogramme de l'image3D
 Pixel3D getMaxPixel()
          Gets the maxPixel attribute of the Image3D object
 float getMean()
          Gets the mean attribute of the Image3D object
 TabUtil getNeighborhood(Image3D ker, int x, int y, int z)
          Gets the neighboring of a pixel, with a kernel
 TabUtil getNeighborhood(int x, int y, int z, int voisx, int voisy, int voisz)
          Gets the voisinage attribute of the Image3D object (sphere)
 TabUtil getNeighborhood3(int x, int y, int z)
          Gets the 3D neighborhood of the pixel in 8 connexicty --> 27 pixels
 TabUtil getNeighborhoodKernel(int[] ker, int nbval, int x, int y, int z, float radx, float rady, float radz)
          Gets the voisinage attribute of the Image3D object
 TabUtil getNeighborhoodLayer(int x, int y, int z, float r0, float r1)
           
 TabUtil getNeighborhoodSphere(int x, int y, int z, float voisx, float voisy, float voisz)
          Gets the neighboring of a pixel (sphere)
abstract  float getPix(float x, float y, float z)
          Gets the pix attribute of the Image3D object
abstract  float getPix(int x, int y, int z)
          Gets the pix attribute of the Image3D object
 float getSigma()
          Gets the sigma attribute of the Image3D object
 int getSizex()
          Gets the sizex attribute of the Image3D object
 int getSizey()
          Gets the sizey attribute of the Image3D object
 int getSizez()
          Gets the sizez attribute of the Image3D object
 ij.ImageStack getStack()
          Constructor for the ImageStack object
 float getSumAbs()
          Gets the sumAbs attribute of the Image3D object
 int getType()
          Gets the type attribute of the Image3D object
 void insert(Image3D vol, int x0, int y0, int z0, boolean moy)
          Insert a 3D image to a specified location
 void kill()
          Kill the Image3D
 double[] radialDistribution(int x0, int y0, int z0, int maxR)
           
 void reset()
           
abstract  void setPix(int x, int y, int z, double value)
          Sets the pix attribute of the Image3D object
 Image3D[] split(int axis, int nb, int overlap)
          Split a image into sub images
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

sizex

protected int sizex
Description of the Field


sizey

protected int sizey
Description of the Field


sizez

protected int sizez
Description of the Field


type

public final int type
Description of the Field


BYTE

public static final int BYTE
Description of the Field

See Also:
Constant Field Values

SHORT

public static final int SHORT
Description of the Field

See Also:
Constant Field Values

FLOAT

public static final int FLOAT
Description of the Field

See Also:
Constant Field Values

max

protected Pixel3D max
Description of the Field


min

protected Pixel3D min
Description of the Field


sigma

protected float sigma
Description of the Field


mean

protected float mean
Description of the Field


centerx

protected float centerx
Description of the Field


centery

protected float centery
Description of the Field


centerz

protected float centerz
Description of the Field


XAXIS

public static final int XAXIS
Description of the Field

See Also:
Constant Field Values

YAXIS

public static final int YAXIS
Description of the Field

See Also:
Constant Field Values

ZAXIS

public static final int ZAXIS
Description of the Field

See Also:
Constant Field Values

stack

protected ij.ImageStack stack
Description of the Field

Constructor Detail

Image3D

public Image3D(int sizex,
               int sizey,
               int sizez,
               int type)
Constructor for the Image3D object

Parameters:
sizex - Description of the Parameter
sizey - Description of the Parameter
sizez - Description of the Parameter
type - Description of the Parameter

Image3D

public Image3D(ij.ImageStack pile)
Constructor for the Image3D object

Parameters:
pile - Description of the Parameter
Method Detail

kill

public void kill()
Kill the Image3D


reset

public void reset()

getStack

public ij.ImageStack getStack()
Constructor for the ImageStack object

Returns:
The stack value

getPix

public abstract float getPix(int x,
                             int y,
                             int z)
Gets the pix attribute of the Image3D object

Parameters:
x - Description of the Parameter
y - Description of the Parameter
z - Description of the Parameter
Returns:
The pix value

getPix

public abstract float getPix(float x,
                             float y,
                             float z)
Gets the pix attribute of the Image3D object

Parameters:
x - Description of the Parameter
y - Description of the Parameter
z - Description of the Parameter
Returns:
The pix value

setPix

public abstract void setPix(int x,
                            int y,
                            int z,
                            double value)
Sets the pix attribute of the Image3D object

Parameters:
x - The new pix value
y - The new pix value
z - The new pix value
value - The new pix value

getSizex

public int getSizex()
Gets the sizex attribute of the Image3D object

Returns:
The sizex value

getSizey

public int getSizey()
Gets the sizey attribute of the Image3D object

Returns:
The sizey value

getSizez

public int getSizez()
Gets the sizez attribute of the Image3D object

Returns:
The sizez value

getType

public int getType()
Gets the type attribute of the Image3D object

Returns:
The type value

getCenterX

public float getCenterX()
Gets the centerX attribute of the Image3D object

Returns:
The centerX value

getCenterY

public float getCenterY()
Gets the centerY attribute of the Image3D object

Returns:
The centerY value

getCenterZ

public float getCenterZ()
Gets the centerZ attribute of the Image3D object

Returns:
The centerZ value

getFloatMaximum

protected double getFloatMaximum()
Gets the floatMaximum attribute of the Image3D object

Returns:
The floatMaximum value

getFloatMinimum

protected double getFloatMinimum()
Gets the floatMinimum attribute of the Image3D object

Returns:
The floatMinimum value

computeMinMax

public void computeMinMax()
Description of the Method


getMean

public float getMean()
Gets the mean attribute of the Image3D object

Returns:
The mean value

getSumAbs

public float getSumAbs()
Gets the sumAbs attribute of the Image3D object

Returns:
The sumAbs value

getSigma

public float getSigma()
Gets the sigma attribute of the Image3D object

Returns:
The sigma value

getMaxPixel

public Pixel3D getMaxPixel()
Gets the maxPixel attribute of the Image3D object

Returns:
The maxPixel value

getNeighborhoodSphere

public TabUtil getNeighborhoodSphere(int x,
                                     int y,
                                     int z,
                                     float voisx,
                                     float voisy,
                                     float voisz)
Gets the neighboring of a pixel (sphere)

Parameters:
x - Coordinate x of the pixel
y - Coordinate y of the pixel
z - Coordinate z of the pixel
voisx - Radius x of the neighboring
voisy - Radius y of the neighboring
voisz - Radius z of the neighboring
Returns:
The neigbor values in a array

getNeighborhood3

public TabUtil getNeighborhood3(int x,
                                int y,
                                int z)
Gets the 3D neighborhood of the pixel in 8 connexicty --> 27 pixels

Parameters:
x - x coordinate
y - y coordinate
z - z coordinate
Returns:
The array with the neighborhood values

getNeighborhood

public TabUtil getNeighborhood(int x,
                               int y,
                               int z,
                               int voisx,
                               int voisy,
                               int voisz)
Gets the voisinage attribute of the Image3D object (sphere)

Parameters:
x - Description of the Parameter
y - Description of the Parameter
z - Description of the Parameter
voisx - Description of the Parameter
voisy - Description of the Parameter
voisz - Description of the Parameter
Returns:
The voisinage value

getNeighborhoodLayer

public TabUtil getNeighborhoodLayer(int x,
                                    int y,
                                    int z,
                                    float r0,
                                    float r1)
Parameters:
x -
y -
z -
r0 -
r1 -
Returns:

radialDistribution

public double[] radialDistribution(int x0,
                                   int y0,
                                   int z0,
                                   int maxR)
Parameters:
x0 -
y0 -
z0 -
maxR -
Returns:

getNeighborhood

public TabUtil getNeighborhood(Image3D ker,
                               int x,
                               int y,
                               int z)
Gets the neighboring of a pixel, with a kernel

Parameters:
x - Coordinate x of the pixel
y - Coordinate y of the pixel
z - Coordinate z of the pixel
ker - The kernel (0 = outside kernel, else inside)
Returns:
The neigbor values in a array

getNeighborhoodKernel

public TabUtil getNeighborhoodKernel(int[] ker,
                                     int nbval,
                                     int x,
                                     int y,
                                     int z,
                                     float radx,
                                     float rady,
                                     float radz)
Gets the voisinage attribute of the Image3D object

Parameters:
ker - Description of the Parameter
nbval -
x - Description of the Parameter
y - Description of the Parameter
z - Description of the Parameter
radx -
radz -
rady -
Returns:
The voisinage value

createKernelEllipsoid

public int[] createKernelEllipsoid(float radx,
                                   float rady,
                                   float radz)
Parameters:
radx -
rady -
radz -
Returns:

insert

public void insert(Image3D vol,
                   int x0,
                   int y0,
                   int z0,
                   boolean moy)
Insert a 3D image to a specified location

Parameters:
vol - the 3D image to be inserted
x0 - the x coordinate of the insertion
y0 - the y coordinate of the insertion
z0 - the z coordinate of the insertion
moy - average with original image

extract

public Image3D extract(int x0,
                       int y0,
                       int z0,
                       int rx,
                       int ry,
                       int rz,
                       boolean sphere)
extract a 3D image from a specified location as the center of crop

Parameters:
x0 - the x coordinate of the center of the extraction
y0 - the y coordinate of the center of the extraction
z0 - the z coordinate of the center of the extraction
rx - radius X of new image
ry - radius Y of new image
rz - radius Z of new image
sphere - extract inside a sphere
Returns:
the cropped image

crop

public Image3D crop(int newzerox,
                    int newzeroy,
                    int newzeroz,
                    int newsizex,
                    int newsizey,
                    int newsizez)
Description of the Method

Parameters:
newzerox - Description of the Parameter
newzeroy - Description of the Parameter
newsizex - Description of the Parameter
newsizey - Description of the Parameter
newsizez - Description of the Parameter
newzeroz - Description of the Parameter
Returns:
Description of the Return Value

split

public Image3D[] split(int axis,
                       int nb,
                       int overlap)
Split a image into sub images

Parameters:
axis - the axis to split along
nb - the number of splitted parts
overlap - the overlap (in pixels)
Returns:
an array of splitted images

createLocalMaximaImage

public abstract Image3D createLocalMaximaImage(int voisx,
                                               int voisy,
                                               int voisz,
                                               boolean keep)
Création d'une image des maxima locaux dans un voisinage donne

Parameters:
voisx - taille voisiange en x
voisy - taille voisiange en y
voisz - taille voisiange en z
keep -
Returns:
Image des maxima locaux

binarisation

public abstract IntImage3D binarisation(int seuilb,
                                        int seuilh)
binarisation de l'image, creation d'une image avec 255 si entre les deux seuils

Parameters:
seuilb - seuil bas
seuilh - seuil haut
Returns:
une Image3D contenant l'image binarisee

getHistogram

public abstract TabUtil getHistogram()
donne l'histogramme de l'image3D

Returns:
l'histogramme