ij3d.image3d
Class RealImage3D

java.lang.Object
  extended by ij3d.image3d.Image3D
      extended by ij3d.image3d.RealImage3D
Direct Known Subclasses:
FHTImage3D

public class RealImage3D
extends Image3D

Description of the Class

Author:
cedric

Field Summary
 
Fields inherited from class ij3d.image3d.Image3D
BYTE, centerx, centery, centerz, FLOAT, max, mean, min, SHORT, sigma, sizex, sizey, sizez, stack, type, XAXIS, YAXIS, ZAXIS
 
Constructor Summary
RealImage3D(Image3D img2copy)
          Constructor copying data from another RealImage3D
RealImage3D(ij.process.ImageProcessor ip)
          Constructor for the RealImage3D object
RealImage3D(ij.ImageStack pile)
          constructeur d'un volume a partir d'un stack
RealImage3D(int sizex, int sizey, int sizez)
          constructeur d'un volume vide (noir)
RealImage3D(int sizex, int sizey, int sizez, float[][] data)
          Constructor for the RealImage3D object
 
Method Summary
 RealImage3D add(RealImage3D img)
          adds a RealImage3D to this one
 RealImage3D add(RealImage3D img, GeomTransform3D transf)
          adds a transformed RealImage3D to this one
 RealImage3D add(RealImage3D img, TabUtil transform)
          adds a transformed RealImage3D to this one
 Image3D addImage(Image3D img, float s, float t)
          Adds a feature to the Image attribute of the RealImage3D object
 Image3D addImage(RealImage3D img, float t)
          Adds a feature to the Image attribute of the RealImage3D object
 RealImage3D addValue(float value)
          adds a given value to all pixels
 RealImage3D applyTransform(GeomTransform3D trans)
          applique une transformation 3D a une image (inversion de la matrice realisee pour trouver le pixel (i,j,k) dans l'image originale)
 RealImage3D autoApplyTransform(GeomTransform3D trans)
          Description of the Method
 IntImage3D binarisation(int seuilb, int seuilh)
          binarisation de l'image
 RealImage3D centerCrop(int newsizex, int newsizey, int newsizez)
          Description of the Method
 RealImage3D createLocalMaximaImage(int voisx, int voisy, int voisz, boolean keep)
          Création d'une image des maxima locaux dans un voisiange donne
 RealImage3D crop(int newcenterx, int newcentery, int newcenterz, int newsizex, int newsizey, int newsizez)
          Description of the Method
 Image3D dilatation3D(int fond, int voisx, int voisy, int voisz)
          base pour la morphologie mathématique binaire (dilatation)
Les objets sont segmentes et ont donc une couleur différente du fond
 RealImage3D divideBy(float div)
          divides all pixels by a value
 Image3D erosion3D(int fond, int voisx, int voisy, int voisz)
          Description of the Method
 Image3D fermeture3D(int fond, int voisx, int voisy, int voisz, int ite)
          Description of the Method
 TabUtil getHistogram()
          donne l'histogramme de l'image3D 32 bits en decoupage de 65 536 bins // attention pas de lien direct entre case et valeur pixel
 double getMaximum()
          donne le maximum de l'image3D
 double getMinimum()
          donne le minimum de l'image3D
 float getPix(float x, float y, float z)
          Gets the trilinear interpolated pixel value at position (x,y,z) as a double
 float getPix(int x, int y, int z)
          Gets the pixel value at position (x,y,z) as a double
 float getPixel(double x, double y, double z)
           
 float getPixel(float x, float y, float z)
          Gets the trilinear interpolated pixel value at position (x,y,z)
 float getPixel(int x, int y, int z)
          Gets the pixel value at position (x,y,z)
 float getPixelTransformedI(double X, double Y, double Z, GeomTransform3D inverttrans)
          Gets the pixel corresponding to the direct application of the transform given
 float getPixelTransformedI(Pixel3D pixel, GeomTransform3D inverttrans)
          Gets the pixel corresponding to the direct application of the transform given
 RealImage3D getPow2Img()
          Gets the pow2Img attribute of the RealImage3D object
 RealImage3D getPow2Img(int sizexmax, int sizeymax, int sizezmax)
          Gets the pow2Img attribute of the RealImage3D object
 ij.ImageStack getStack()
          Gets the stack attribute of the RealImage3D object
 float getTransformPixel(Pixel3D pixel, GeomTransform3D trans)
          Gets the pixel corresponding to the pixel given if the transform is applied (inversion of matrice)
 boolean isLocalMaximum(int x, int y, int z, int voisx, int voisy, int voisz)
          dit si le pixel donne est un maximum local avec un voisinage donne
 RealImage3D maximumFilter(int voisx, int voisy, int voisz)
          filtre le volume grace a un filtre maximum 3D
 Image3D medianFilter(int voisx, int voisy, int voisz)
          filtre le volume grace a un filtre median 3D
 Image3D minimumFilter(int voisx, int voisy, int voisz)
          filtre le volume grace a un filtre minimum 3D
 RealImage3D multiplyBy(float mult)
          multiplies all pixels by a given value
 RealImage3D multiplyBy(Image3D mult)
           
 Image3D nonLinearLaplacianFilter(int voisx, int voisy, int voisz)
          filtre le volume grace a un filtre laplacien non lineaire
 Image3D ouverture3D(int fond, int voisx, int voisy, int voisz, int ite)
          Description of the Method
 RealImage3D project(int axis)
          Description of the Method
 RealImage3D project(Vector3D V, Vector3D C, boolean moy)
          Description of the Method
 ij.process.FloatProcessor projection(Vector3D V, Vector3D C, boolean moy)
          Description of the Method
 ij.process.FloatProcessor projectionInterpolated(Vector3D W, boolean moy)
          Projection by interpolation
 void putPixel(int x, int y, int z, double value)
          Description of the Method
 void putPixel(int x, int y, int z, float value)
          Sets the pixel value at position (x,y,z)
 RealImage3D resetImage()
          Description of the Method
 void setPix(int x, int y, int z, double value)
          Sets the pixel value at position (x,y,z) as a double
 void setSizes(int sx, int sy, int sz)
          Sets the sizes attribute of the RealImage3D object
 Image3D tophatFilter(int voisx, int voisy, int voisz)
          filtre le volume grace a un filtre top hat
 
Methods inherited from class ij3d.image3d.Image3D
computeMinMax, createKernelEllipsoid, extract, getCenterX, getCenterY, getCenterZ, getFloatMaximum, getFloatMinimum, getMaxPixel, getMean, getNeighborhood, getNeighborhood, getNeighborhood3, getNeighborhoodKernel, getNeighborhoodLayer, getNeighborhoodSphere, getSigma, getSizex, getSizey, getSizez, getSumAbs, getType, insert, kill, radialDistribution, reset, split
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

RealImage3D

public RealImage3D(int sizex,
                   int sizey,
                   int sizez)
constructeur d'un volume vide (noir)

Parameters:
sizex - taille du volume en x
sizey - taille du volume en y
sizez - taille du volume en z

RealImage3D

public RealImage3D(int sizex,
                   int sizey,
                   int sizez,
                   float[][] data)
Constructor for the RealImage3D object

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

RealImage3D

public RealImage3D(ij.ImageStack pile)
constructeur d'un volume a partir d'un stack

Parameters:
pile - stack en entree

RealImage3D

public RealImage3D(ij.process.ImageProcessor ip)
Constructor for the RealImage3D object

Parameters:
ip - Description of the Parameter

RealImage3D

public RealImage3D(Image3D img2copy)
Constructor copying data from another RealImage3D

Parameters:
img2copy - RealImage3D to copy
Method Detail

setSizes

public void setSizes(int sx,
                     int sy,
                     int sz)
Sets the sizes attribute of the RealImage3D object

Parameters:
sx - The new sizes value
sy - The new sizes value
sz - The new sizes value

getPix

public float getPix(int x,
                    int y,
                    int z)
Gets the pixel value at position (x,y,z) as a double

Specified by:
getPix in class Image3D
Parameters:
x - coordinate on X axis
y - coordinate on Y axis
z - coordinate on Z axis
Returns:
The pixel value

getPixel

public float getPixel(int x,
                      int y,
                      int z)
Gets the pixel value at position (x,y,z)

Parameters:
x - coordinate on X axis
y - coordinate on Y axis
z - coordinate on Z axis
Returns:
The pixel value

getPix

public float getPix(float x,
                    float y,
                    float z)
Gets the trilinear interpolated pixel value at position (x,y,z) as a double

Specified by:
getPix in class Image3D
Parameters:
x - coordinate on X axis
y - coordinate on Y axis
z - coordinate on Z axis
Returns:
The pixel value

getPixel

public float getPixel(float x,
                      float y,
                      float z)
Gets the trilinear interpolated pixel value at position (x,y,z)

Parameters:
x - coordinate on X axis
y - coordinate on Y axis
z - coordinate on Z axis
Returns:
The pixel value

getPixel

public float getPixel(double x,
                      double y,
                      double z)
Parameters:
x -
y -
z -
Returns:

setPix

public void setPix(int x,
                   int y,
                   int z,
                   double value)
Sets the pixel value at position (x,y,z) as a double

Specified by:
setPix in class Image3D
Parameters:
x - coordinate on X axis
y - coordinate on Y axis
z - coordinate on Z axis
value - The pixel value

putPixel

public void putPixel(int x,
                     int y,
                     int z,
                     float value)
Sets the pixel value at position (x,y,z)

Parameters:
x - coordinate on X axis
y - coordinate on Y axis
z - coordinate on Z axis
value - The pixel value

putPixel

public void putPixel(int x,
                     int y,
                     int z,
                     double value)
Description of the Method

Parameters:
x - Description of the Parameter
y - Description of the Parameter
z - Description of the Parameter
value - Description of the Parameter

getStack

public ij.ImageStack getStack()
Gets the stack attribute of the RealImage3D object

Overrides:
getStack in class Image3D
Returns:
The stack value

getMaximum

public double getMaximum()
donne le maximum de l'image3D

Returns:
la valeur maximum de l'image3D

getMinimum

public double getMinimum()
donne le minimum de l'image3D

Returns:
la valeur minimum de l'image3D

getPow2Img

public RealImage3D getPow2Img()
Gets the pow2Img attribute of the RealImage3D object

Returns:
The pow2Img value

getPow2Img

public RealImage3D getPow2Img(int sizexmax,
                              int sizeymax,
                              int sizezmax)
Gets the pow2Img attribute of the RealImage3D object

Parameters:
sizexmax - Description of the Parameter
sizeymax - Description of the Parameter
sizezmax - Description of the Parameter
Returns:
The pow2Img value

createLocalMaximaImage

public RealImage3D createLocalMaximaImage(int voisx,
                                          int voisy,
                                          int voisz,
                                          boolean keep)
Création d'une image des maxima locaux dans un voisiange donne

Specified by:
createLocalMaximaImage in class Image3D
Parameters:
voisx - taille voisiange en x
voisy - taille voisiange en y
voisz - taille voisiange en z
keep -
Returns:
Image des maxima locaux

isLocalMaximum

public boolean isLocalMaximum(int x,
                              int y,
                              int z,
                              int voisx,
                              int voisy,
                              int voisz)
dit si le pixel donne est un maximum local avec un voisinage donne

Parameters:
x - coordonnee en x du pixel
y - coordonnee en y du pixel
z - coordonnee en z du pixel
voisx - voisinage en x
voisy - voisinage en y
voisz - voisinage en z
Returns:
vrai si le pixel est maximum local dans le voisinage donne

binarisation

public IntImage3D binarisation(int seuilb,
                               int seuilh)
binarisation de l'image

Specified by:
binarisation in class Image3D
Parameters:
seuilb - Description of the Parameter
seuilh - Description of the Parameter
Returns:
une Image3D contenant l'image binarisee

getHistogram

public TabUtil getHistogram()
donne l'histogramme de l'image3D 32 bits en decoupage de 65 536 bins // attention pas de lien direct entre case et valeur pixel

Specified by:
getHistogram in class Image3D
Returns:
l'histogramme

addImage

public Image3D addImage(Image3D img,
                        float s,
                        float t)
Adds a feature to the Image attribute of the RealImage3D object

Parameters:
img - The feature to be added to the Image attribute
s - The feature to be added to the Image attribute
t - The feature to be added to the Image attribute
Returns:
Description of the Return Value

addImage

public Image3D addImage(RealImage3D img,
                        float t)
Adds a feature to the Image attribute of the RealImage3D object

Parameters:
img - The feature to be added to the Image attribute
t - The feature to be added to the Image attribute
Returns:
Description of the Return Value

add

public RealImage3D add(RealImage3D img)
adds a RealImage3D to this one

Parameters:
img - RealImage3d to add
Returns:
this image3d to which an other image3d has been added

add

public RealImage3D add(RealImage3D img,
                       TabUtil transform)
adds a transformed RealImage3D to this one

Parameters:
img - RealImage3d to add
transform - 3D transform to apply to the image given [tx ty tz rx ry rz]
Returns:
this image3d to which an other image3d has been added

add

public RealImage3D add(RealImage3D img,
                       GeomTransform3D transf)
adds a transformed RealImage3D to this one

Parameters:
img - RealImage3d to add
transf - 3D transform to apply to the image given
Returns:
this image3d to which an other image3d has been added

divideBy

public RealImage3D divideBy(float div)
divides all pixels by a value

Parameters:
div - value by which dividing all pixels
Returns:
the resulting image (image definitively modified)

multiplyBy

public RealImage3D multiplyBy(float mult)
multiplies all pixels by a given value

Parameters:
mult - value by which multiplying all pixels
Returns:
the resulting image (image definitively modified)

multiplyBy

public RealImage3D multiplyBy(Image3D mult)
Parameters:
mult -
Returns:

addValue

public RealImage3D addValue(float value)
adds a given value to all pixels

Parameters:
value - value to add to all pixels
Returns:
the resulting image (image definitively modified)

applyTransform

public RealImage3D applyTransform(GeomTransform3D trans)
applique une transformation 3D a une image (inversion de la matrice realisee pour trouver le pixel (i,j,k) dans l'image originale)

Parameters:
trans - Description of the Parameter
Returns:
Description of the Return Value

autoApplyTransform

public RealImage3D autoApplyTransform(GeomTransform3D trans)
Description of the Method

Parameters:
trans - Description of the Parameter
Returns:
Description of the Return Value

getTransformPixel

public float getTransformPixel(Pixel3D pixel,
                               GeomTransform3D trans)
Gets the pixel corresponding to the pixel given if the transform is applied (inversion of matrice)

Parameters:
pixel - Description of the Parameter
trans - Description of the Parameter
Returns:
The transformPixel value

getPixelTransformedI

public float getPixelTransformedI(Pixel3D pixel,
                                  GeomTransform3D inverttrans)
Gets the pixel corresponding to the direct application of the transform given

Parameters:
pixel - coordinates of the original pixel
inverttrans - 3D transform inverted
Returns:
The pixel value via transformation

getPixelTransformedI

public float getPixelTransformedI(double X,
                                  double Y,
                                  double Z,
                                  GeomTransform3D inverttrans)
Gets the pixel corresponding to the direct application of the transform given

Parameters:
X - coordinate of original pixel on X Axis
Y - coordinate of original pixel on Y Axis
Z - coordinate of original pixel on Z Axis
inverttrans - 3D transform inverted
Returns:
The pixel value via transformation

centerCrop

public RealImage3D centerCrop(int newsizex,
                              int newsizey,
                              int newsizez)
Description of the Method

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

crop

public RealImage3D crop(int newcenterx,
                        int newcentery,
                        int newcenterz,
                        int newsizex,
                        int newsizey,
                        int newsizez)
Description of the Method

Overrides:
crop in class Image3D
Parameters:
newcenterx - Description of the Parameter
newcentery - Description of the Parameter
newcenterz - Description of the Parameter
newsizex - Description of the Parameter
newsizey - Description of the Parameter
newsizez - Description of the Parameter
Returns:
Description of the Return Value

resetImage

public RealImage3D resetImage()
Description of the Method

Returns:
Description of the Return Value

medianFilter

public Image3D medianFilter(int voisx,
                            int voisy,
                            int voisz)
filtre le volume grace a un filtre median 3D

Parameters:
voisx - rayon du voisinage en x
voisy - rayon du voisinage en y
voisz - rayon du voisinage en z
Returns:
Image3D contenant le volume filtre par un filtre median

maximumFilter

public RealImage3D maximumFilter(int voisx,
                                 int voisy,
                                 int voisz)
filtre le volume grace a un filtre maximum 3D

Parameters:
voisx - rayon du voisinage en x
voisy - rayon du voisinage en y
voisz - rayon du voisinage en z
Returns:
Image3D contenant le volume filtre par un filtre median

minimumFilter

public Image3D minimumFilter(int voisx,
                             int voisy,
                             int voisz)
filtre le volume grace a un filtre minimum 3D

Parameters:
voisx - rayon du voisinage en x
voisy - rayon du voisinage en y
voisz - rayon du voisinage en z
Returns:
Image3D contenant le volume filtre par un filtre median

tophatFilter

public Image3D tophatFilter(int voisx,
                            int voisy,
                            int voisz)
filtre le volume grace a un filtre top hat

Parameters:
voisx - rayon du voisinage en x
voisy - rayon du voisinage en y
voisz - rayon du voisinage en z
Returns:
Image3D contenant le volume filtre par un filtre top hat

nonLinearLaplacianFilter

public Image3D nonLinearLaplacianFilter(int voisx,
                                        int voisy,
                                        int voisz)
filtre le volume grace a un filtre laplacien non lineaire

Parameters:
voisx - Description of the Parameter
voisy - Description of the Parameter
voisz - Description of the Parameter
Returns:
Description of the Return Value

dilatation3D

public Image3D dilatation3D(int fond,
                            int voisx,
                            int voisy,
                            int voisz)
base pour la morphologie mathématique binaire (dilatation)
Les objets sont segmentes et ont donc une couleur différente du fond

Parameters:
fond - niveau de gris du fond
voisx - voisinage en x
voisy - voisinage en y
voisz - voisinage en z
Returns:
image modifiée

erosion3D

public Image3D erosion3D(int fond,
                         int voisx,
                         int voisy,
                         int voisz)
Description of the Method

Parameters:
fond - Description of the Parameter
voisx - Description of the Parameter
voisy - Description of the Parameter
voisz - Description of the Parameter
Returns:
Description of the Return Value

ouverture3D

public Image3D ouverture3D(int fond,
                           int voisx,
                           int voisy,
                           int voisz,
                           int ite)
Description of the Method

Parameters:
voisx - Description of the Parameter
voisy - Description of the Parameter
voisz - Description of the Parameter
ite - Description of the Parameter
fond - Description of the Parameter
Returns:
Description of the Return Value

fermeture3D

public Image3D fermeture3D(int fond,
                           int voisx,
                           int voisy,
                           int voisz,
                           int ite)
Description of the Method

Parameters:
voisx - Description of the Parameter
voisy - Description of the Parameter
voisz - Description of the Parameter
ite - Description of the Parameter
fond - Description of the Parameter
Returns:
Description of the Return Value

project

public RealImage3D project(int axis)
Description of the Method

Parameters:
axis - Description of the Parameter
Returns:
Description of the Return Value

project

public RealImage3D project(Vector3D V,
                           Vector3D C,
                           boolean moy)
Description of the Method

Parameters:
V - Description of the Parameter
C - Description of the Parameter
moy - Description of the Parameter
Returns:
Description of the Return Value

projection

public ij.process.FloatProcessor projection(Vector3D V,
                                            Vector3D C,
                                            boolean moy)
Description of the Method

Parameters:
V - Description of the Parameter
C - Description of the Parameter
moy - Description of the Parameter
Returns:
Description of the Return Value

projectionInterpolated

public ij.process.FloatProcessor projectionInterpolated(Vector3D W,
                                                        boolean moy)
Projection by interpolation

Parameters:
W - Direction of the projection
moy - Mean projection or sum
Returns:
Projected image