@Deprecated public class IntImage3D extends Image3D
Constructor and Description |
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IntImage3D(ImagePlus plus)
Deprecated.
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IntImage3D(ImageStack stack)
Deprecated.
constructor from a ImageStack
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IntImage3D(int sizex,
int sizey,
int sizez)
Deprecated.
constructor (black image)
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IntImage3D(int sizex,
int sizey,
int sizez,
int ty)
Deprecated.
Constructor for the IntImage3D object
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Modifier and Type | Method and Description |
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IntImage3D |
adaptiveFilter(float radx,
float rady,
float radz,
int nbcpus)
Deprecated.
Adaptive Filter in 3D (expermimental) Take 7 neighborhood, compute mean
and std dev Assign mean of neighborhood with lowest std dev
|
Image3D |
addImage(IntImage3D img,
float s)
Deprecated.
Adds a feature to the Image attribute of the IntImage3D object
|
Image3D |
addValue(int s)
Deprecated.
Description of the Method
|
IntImage3D |
binarisation(int lowThreshold,
int highThreshold)
Deprecated.
binarisation de l'image, creation d'une image avec 255 si entre les deux
seuils
|
ImageInt |
binaryReconstruct(ImageInt base)
Deprecated.
Description of the Method
|
ImageInt |
binaryReconstructByObjects(ImageInt base)
Deprecated.
|
IntImage3D |
closing3D(float voisx,
float voisy,
float voisz,
int ite,
boolean normal)
Deprecated.
Fermeture binaire 3D, normalement les objets sont noir sur fond blanc
|
IntImage3D |
closing3D(Image3D ker,
int ite,
boolean normal)
Deprecated.
Fermeture binaire 3D avec kernel, normalement les objets sont noir sur
fond blanc
|
IntImage3D |
closing3D(int voisx,
int voisy,
int voisz,
int ite)
Deprecated.
Fermeture binaire 3D, normalement les objets sont noir sur fond blanc
|
RealImage3D |
computeHessianDerivative(int value)
Deprecated.
compute the hessian derivative (to validate)
|
IntImage3D |
createImageSameSize3D()
Deprecated.
|
IntImage3D |
createLocalMaximaImage(float voisx,
float voisy,
float voisz,
boolean keep)
Deprecated.
Création d'une image des maxima locaux dans un voisinage donne
|
IntImage3D |
createLocalMaximaImage(float voisx,
float voisy,
float voisz,
int th,
boolean keep)
Deprecated.
Création d'une image des maxima locaux dans un voisiange donne
|
IntImage3D |
dilatation3D(float radx,
float rady,
float radz,
boolean black)
Deprecated.
3D dilatation
|
IntImage3D |
dilatation3D(Image3D ker,
boolean black)
Deprecated.
3D dilatation with kernel
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protected IntImage3D |
dilatationConditionGris(IntImage3D base,
int voisx,
int voisy,
int voisz)
Deprecated.
Dilatation par rapport a une image de base
|
IntImage3D |
erosion3D(float voisx,
float voisy,
float voisz,
boolean normal)
Deprecated.
Erosion binaire 3D, normalement les objets sont noir sur fond blanc
|
IntImage3D |
erosion3D(Image3D ker)
Deprecated.
Erosion binaire 3D avec kernel, normalement les objets sont noir sur fond
blanc
|
IntImage3D |
erosion3D(Image3D ker,
boolean normal)
Deprecated.
Erosion binaire 3D avec kernel, normalement les objets sont noir sur fond
blanc
|
IntImage3D |
erosion3D(int voisx,
int voisy,
int voisz)
Deprecated.
Erosion binaire 3D, normalement les objets sont noir sur fond blanc
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void |
extendHisto()
Deprecated.
extension de l'histogramme de l'image 8 bits
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IntImage3D |
fillHoles3D(int background,
int object)
Deprecated.
Fill holes for a binary image
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void |
filterGeneric(IntImage3D out,
float radx,
float rady,
float radz,
int zmin,
int zmax,
int filter)
Deprecated.
3D filter using threads
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protected void |
flood3D(IntImage3D base,
int x0,
int y0,
int z0,
int val)
Deprecated.
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ArrayUtil |
getColumn(int x,
int y,
int z)
Deprecated.
int donne une ligne de l'image3D
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int |
getCount(int sb,
int sh)
Deprecated.
Gets the count attribute of the IntImage3D object
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HistogramUtil |
getHistogram()
Deprecated.
donne l'histogramme de l'image3D 16 bits
|
int |
getMaximum()
Deprecated.
donne le maximum de l'image3D
|
int |
getMean(int sb,
int sh)
Deprecated.
Gets the meanValue attribute of the IntImage3D object
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int |
getMinAboveValue(int value)
Deprecated.
Gets the minAboveValue attribute of the FishImage3D object
|
int |
getMinimum()
Deprecated.
donne le minimum de l'image3D
|
float |
getPix(float x,
float y,
float z)
Deprecated.
Gets the pix attribute of the IntImage3D object
|
float |
getPix(int x,
int y,
int z)
Deprecated.
Gets the pix attribute of the IntImage3D object
|
float |
getPix(Voxel3D vox,
boolean b)
Deprecated.
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int |
getPixel(double x,
double y,
double z)
Deprecated.
|
int |
getPixel(float x,
float y,
float z)
Deprecated.
Gets the pixel attribute of the IntImage3D object with tri-linear
interpolation
|
int |
getPixel(int x,
int y,
int z)
Deprecated.
recupere la valeur du pixel de coordonnees (x,y,z)
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int |
getPixel(Point3D point,
boolean interpolate)
Deprecated.
Gets the pixel attribute of the IntImage3D object
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int |
getPixel(Vector3D vector,
boolean interpolate)
Deprecated.
Gets the pixel attribute of the IntImage3D object
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int |
getPixel(Voxel3D point,
boolean interpolate)
Deprecated.
Gets the pixel attribute of the IntImage3D object
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double[] |
getPixelMoments(int x,
int y,
int z,
int radXY,
int radZ)
Deprecated.
Gets the pixelMoments attribute of the IntImage3D object
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ArrayUtil |
getProf(int x,
int y,
int z)
Deprecated.
donne une ligne en Z dans l'image 3D
|
ArrayUtil |
getRow(int x,
int y,
int z)
Deprecated.
donne une ligne de l'image3D
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double |
getSigma(int sb,
int sh)
Deprecated.
Gets the sigma attribute of the IntImage3D object
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ImageStack |
getStack()
Deprecated.
Gets the ImageStack associated with the 3D image
|
IntImage3D |
gradient(int axis)
Deprecated.
The gradient of the image in a given direction (sobel)
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IntImage3D |
grayDilatation(IntImage3D ker)
Deprecated.
|
IntImage3D |
grayErosion(IntImage3D ker)
Deprecated.
|
IntImage3D |
grayReconstruction(IntImage3D base)
Deprecated.
|
IntImage3D |
hitOrMiss(int obj,
int fond,
Image3D ker)
Deprecated.
|
boolean |
isBinary(int background)
Deprecated.
|
boolean |
isLocalMaximum(int x,
int y,
int z,
float voisx,
float voisy,
float voisz)
Deprecated.
dit si le pixel donne est un maximum local avec un voisinage donne
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RealImage3D |
logMath()
Deprecated.
Compute the log of the image
|
IntImage3D |
max(IntImage3D ima)
Deprecated.
|
IntImage3D |
maximumFilter(float radx,
float rady,
float radz)
Deprecated.
3D maximum filter
|
IntImage3D |
medianFilter(float radx,
float rady,
float radz)
Deprecated.
3D median filter
|
IntImage3D |
min(IntImage3D ima)
Deprecated.
|
IntImage3D |
minimumFilter(float radx,
float rady,
float radz)
Deprecated.
3D minimum filter
|
int |
nbConnexite2D(int val,
int z)
Deprecated.
Description of the Method
|
IntImage3D |
nbNeighbor(int obj)
Deprecated.
Number of neighborhood pixels
|
IntImage3D |
nlLaplacien(int radx,
int rady,
int radz)
Deprecated.
3D non linear laplacien
|
IntImage3D |
nonLinearLaplacianFilter(int radx,
int rady,
int radz)
Deprecated.
3D non linear laplacian (version 2)
|
IntImage3D |
opening3D(Image3D ker,
int ite)
Deprecated.
Ouverture binaire 3D avec kernel, normalement les objets sont noir sur
fond blanc
|
IntImage3D |
opening3D(Image3D ker,
int ite,
boolean normal)
Deprecated.
Ouverture binaire 3D avec kernel, normalement les objets sont noir sur
fond blanc
|
IntImage3D |
opening3D(int voisx,
int voisy,
int voisz,
int ite)
Deprecated.
Ouverture binaire 3D, normalement les objets sont noir sur fond blanc
|
IntImage3D |
opening3D(int voisx,
int voisy,
int voisz,
int ite,
boolean normal)
Deprecated.
Ouverture binaire 3D, normalement les objets sont noir sur fond blanc
|
protected IntImage3D |
projection(int val,
int axe,
int p1,
int p2)
Deprecated.
Average projection
|
IntImage3D |
projectionX(int val)
Deprecated.
Description of the Method
|
IntImage3D |
projectionY(int val)
Deprecated.
Description of the Method
|
IntImage3D |
projectionZ(int val)
Deprecated.
Description of the Method
|
IntImage3D |
projectionZ(int val,
int p1,
int p2)
Deprecated.
Description of the Method
|
void |
propagation(IntImage3D base,
int abs,
int ord,
int prof,
int val,
int nval)
Deprecated.
Propagation of a value to connected pixels
|
void |
propagation27(int xx,
int yy,
int zz,
int val,
int nval)
Deprecated.
Propagation of a value to connected pixels
|
protected void |
propagation2D(int abs,
int ord,
int prof,
int val,
int nval)
Deprecated.
Description of the Method
|
void |
propagation6(int xx,
int yy,
int zz,
int val,
int nval)
Deprecated.
Propagation of a value to connected pixels
|
protected void |
propagationConditionnelle(IntImage3D base,
int abs,
int ord,
int prof,
int val)
Deprecated.
Description of the Method
|
void |
putPixel(int x,
int y,
int z,
double value)
Deprecated.
|
void |
putPixel(int x,
int y,
int z,
int value)
Deprecated.
donne une valeur au pixel de coordonnees (x,y,z)
|
void |
replacePixelsValue(int val,
int rep)
Deprecated.
Replace a pixel value by another
|
void |
replacePixelsValue(int val,
int rep,
Object3DVoxels obj)
Deprecated.
Replace a pixel value by another within a specified object
|
IntImage3D |
RH_Maxima(int R,
int H)
Deprecated.
Méthode du RH maxima
|
void |
setPix(int x,
int y,
int z,
double value)
Deprecated.
Sets the pix attribute of the IntImage3D object
|
int |
snr3D()
Deprecated.
Description of the Method
|
IntImage3D |
sobelFilter()
Deprecated.
Sobel-like filtering in 3D
|
IntImage3D |
tapper(int r0x,
int r0y,
int r0z)
Deprecated.
Tappering - smooth towards background
|
IntImage3D |
tophatFilter(int radx,
int rady,
int radz)
Deprecated.
TopHat Filter to remove local background Enhance spots
|
RealImage3D |
varianceFilter(float radx,
float rady,
float radz)
Deprecated.
Variance Filter in 3D
|
IntImage3D |
watershed()
Deprecated.
Watershed algorithm starting with a seed image where seed > 0
|
computeMinMax, createKernelEllipsoid, crop, crossCorrelationNormalized, extract, getCenterX, getCenterY, getCenterZ, getFloatMaximum, getFloatMinimum, getLinePixelValue, getLinePixelValue, getMaxPixel, getMean, getNbPixel, getNeighborhood, getNeighborhood, getNeighborhood3x3x3, getNeighborhoodCross3D, getNeighborhoodGrayKernelAdd, getNeighborhoodGrayKernelMinus, getNeighborhoodKernel, getNeighborhoodLayer, getNeighborhoodLayer, getNeighborhoodSphere, getNeighborhoodSphere, getPlus, getSigma, getSizex, getSizey, getSizez, getSumAbs, getType, insert, kill, radialDistribution, radialDistribution, reset, reset, setShowStatus, split
public IntImage3D(int sizex, int sizey, int sizez)
sizex
- size x of 3D imagesizey
- size y of 3D imagesizez
- size z of 3D imagepublic IntImage3D(int sizex, int sizey, int sizez, int ty)
sizex
- size x of 3D imagesizey
- size x of 3D imagesizez
- size x of 3D imagety
- Data typepublic IntImage3D(ImageStack stack)
stack
- IJstackpublic IntImage3D(ImagePlus plus)
public IntImage3D createImageSameSize3D()
public ImageStack getStack()
public IntImage3D medianFilter(float radx, float rady, float radz)
radx
- Radius of neighborhood in xrady
- Radius of neighborhood in yradz
- Radius of neighborhood in zpublic void filterGeneric(IntImage3D out, float radx, float rady, float radz, int zmin, int zmax, int filter)
out
- radx
- Radius of mean filter in xrady
- Radius of mean filter in yradz
- Radius of mean filter in zzmin
- zmax
- filter
- public RealImage3D varianceFilter(float radx, float rady, float radz)
radx
- radius in xrady
- radius in yradz
- radius in zpublic IntImage3D adaptiveFilter(float radx, float rady, float radz, int nbcpus)
radx
- radz
- rady
- public IntImage3D maximumFilter(float radx, float rady, float radz)
radx
- Radius of mean filter in xrady
- Radius of mean filter in yradz
- Radius of mean filter in zpublic double[] getPixelMoments(int x, int y, int z, int radXY, int radZ)
x
- x coordinate of pixely
- y coordinate of pixelz
- z coordinate of pixelradXY
- Description of the ParameterradZ
- Description of the Parameterpublic IntImage3D minimumFilter(float radx, float rady, float radz)
radx
- Radius of mean filter in xrady
- Radius of mean filter in yradz
- Radius of mean filter in zpublic IntImage3D tophatFilter(int radx, int rady, int radz)
radx
- rayon du voisinage en xrady
- rayon du voisinage en yradz
- rayon du voisinage en zpublic IntImage3D nlLaplacien(int radx, int rady, int radz)
radx
- Radius of mean filter in xrady
- Radius of mean filter in yradz
- Radius of mean filter in zpublic IntImage3D nonLinearLaplacianFilter(int radx, int rady, int radz)
radx
- rayon du voisinage en xrady
- rayon du voisinage en yradz
- rayon du voisinage en zpublic IntImage3D dilatation3D(float radx, float rady, float radz, boolean black)
radx
- voisinage en xrady
- voisinage en yradz
- voisinage en zblack
- black objects (0)public IntImage3D dilatation3D(Image3D ker, boolean black)
ker
- The kernel imageblack
- black objects (0)public IntImage3D erosion3D(float voisx, float voisy, float voisz, boolean normal)
voisx
- voisinage en xvoisy
- voisinage en yvoisz
- voisinage en znormal
- Vrai si obj noir sur blanc, faux sinonpublic IntImage3D erosion3D(Image3D ker, boolean normal)
normal
- Vrai si obj noir sur blanc, faux sinonker
- Le kernel (>0 inside kernel, 0 outside kernel)public IntImage3D erosion3D(int voisx, int voisy, int voisz)
voisx
- voisinage en xvoisy
- voisinage en yvoisz
- voisinage en zpublic IntImage3D erosion3D(Image3D ker)
ker
- Le kernel (>0 inside kernel, 0 outside kernel)public IntImage3D hitOrMiss(int obj, int fond, Image3D ker)
public IntImage3D grayDilatation(IntImage3D ker)
ker
- public IntImage3D grayErosion(IntImage3D ker)
ker
- public IntImage3D opening3D(int voisx, int voisy, int voisz, int ite, boolean normal)
voisx
- voisinage en xvoisy
- voisinage en yvoisz
- voisinage en zite
- Taille de l'ouverturenormal
- Vrai si obj noir sur blanc, faux sinonpublic IntImage3D opening3D(Image3D ker, int ite, boolean normal)
normal
- Vrai si obj noir sur blanc, faux sinonker
- Noyau (>0 inside kernel, 0 outside kernel)ite
- Description of the Parameterpublic IntImage3D opening3D(int voisx, int voisy, int voisz, int ite)
voisx
- voisinage en xvoisy
- voisinage en yvoisz
- voisinage en zite
- Taille de l'ouverturepublic IntImage3D opening3D(Image3D ker, int ite)
ite
- Taille de l'ouvertureker
- Noyau (>0 inside kernel, 0 outside kernel)public IntImage3D closing3D(float voisx, float voisy, float voisz, int ite, boolean normal)
voisx
- voisinage en xvoisy
- voisinage en yvoisz
- voisinage en zite
- Taille de la fermeturenormal
- Vrai si obj noir sur blanc, faux sinonpublic IntImage3D closing3D(Image3D ker, int ite, boolean normal)
normal
- Vrai si obj noir sur blanc, faux sinonker
- Noyau (>0 inside kernel, 0 outside kernel)ite
- Description of the Parameterpublic IntImage3D closing3D(int voisx, int voisy, int voisz, int ite)
voisx
- voisinage en xvoisy
- voisinage en yvoisz
- voisinage en zite
- Taille de l'ouverturepublic int getPixel(int x, int y, int z)
x
- coordonnee en xy
- coordonnee en yintz
- coordonnee en zpublic int getPixel(Point3D point, boolean interpolate)
point
- Description of the Parameterinterpolate
- Description of the Parameterpublic int getPixel(Voxel3D point, boolean interpolate)
point
- Description of the Parameterinterpolate
- Description of the Parameterpublic int getPixel(Vector3D vector, boolean interpolate)
vector
- Description of the Parameterinterpolate
- Description of the Parameterpublic int getPixel(float x, float y, float z)
x
- x coordinate (float)y
- y coordinate (float)z
- z coordinate (float)public int getPixel(double x, double y, double z)
x
- y
- z
- public float getPix(int x, int y, int z)
public float getPix(float x, float y, float z)
public float getPix(Voxel3D vox, boolean b)
public void setPix(int x, int y, int z, double value)
public final void putPixel(int x, int y, int z, int value)
x
- coordonnee en xy
- coordonnee en yz
- coordonnee en zvalue
- valeur du pixelpublic final void putPixel(int x, int y, int z, double value)
public IntImage3D binarisation(int lowThreshold, int highThreshold)
binarisation
in class Image3D
lowThreshold
- seuil bashighThreshold
- seuil hautpublic boolean isBinary(int background)
background
- public void extendHisto()
public int getMaximum()
public int getMinimum()
public int getMinAboveValue(int value)
value
- Description of the Parameterpublic int getMean(int sb, int sh)
sb
- Description of the Parametersh
- Description of the Parameterpublic int getCount(int sb, int sh)
sb
- Description of the Parametersh
- Description of the Parameterpublic IntImage3D tapper(int r0x, int r0y, int r0z)
r0x
- radius xr0y
- radius yr0z
- radius zpublic double getSigma(int sb, int sh)
sb
- Description of the Parametersh
- Description of the Parameterpublic ArrayUtil getRow(int x, int y, int z)
x
- coordonnee en x du pixel de departy
- coordonnee en y du pixel de departz
- coordonnee en z du pixel de departpublic ArrayUtil getColumn(int x, int y, int z)
x
- coordonnee en x du pixel de departy
- coordonnee en y du pixel de departz
- coordonnee en z du pixel de departpublic ArrayUtil getProf(int x, int y, int z)
x
- coordonnee en x du pixel de departy
- coordonnee en y du pixel de departz
- coordonnee en z du pixel de departpublic HistogramUtil getHistogram()
getHistogram
in class Image3D
public boolean isLocalMaximum(int x, int y, int z, float voisx, float voisy, float voisz)
x
- coordonnee en x du pixely
- coordonnee en y du pixelz
- coordonnee en z du pixelvoisx
- voisinage en xvoisy
- voisinage en yvoisz
- voisinage en zpublic IntImage3D createLocalMaximaImage(float voisx, float voisy, float voisz, boolean keep)
createLocalMaximaImage
in class Image3D
voisx
- taille voisinage en xvoisy
- taille voisinage en yvoisz
- taille voisinage en zkeep
- public IntImage3D createLocalMaximaImage(float voisx, float voisy, float voisz, int th, boolean keep)
voisx
- taille voisinage en xvoisy
- taille voisinage en yvoisz
- taille voisinage en zth
- threshold image (255)keep
- public Image3D addImage(IntImage3D img, float s)
img
- The feature to be added to the Image attributes
- The feature to be added to the Image attributepublic Image3D addValue(int s)
s
- Description of the Parameterpublic IntImage3D min(IntImage3D ima)
ima
- public IntImage3D max(IntImage3D ima)
public RealImage3D logMath()
public void replacePixelsValue(int val, int rep)
val
- the value to be replacedrep
- the new valuepublic void replacePixelsValue(int val, int rep, Object3DVoxels obj)
val
- the value to be replacedrep
- the new valueobj
- the objectprotected IntImage3D dilatationConditionGris(IntImage3D base, int voisx, int voisy, int voisz)
base
- Imagevoisx
- taille voisinage en xvoisy
- taille voisinage en yvoisz
- taille voisinage en zprotected void flood3D(IntImage3D base, int x0, int y0, int z0, int val)
protected void propagationConditionnelle(IntImage3D base, int abs, int ord, int prof, int val)
base
- Description of the Parameterabs
- Description of the Parameterord
- Description of the Parameterval
- Description of the Parameterprof
- Description of the Parameterpublic void propagation27(int xx, int yy, int zz, int val, int nval)
xx
- x of the first pointyy
- y of the first pointzz
- z of the first pointval
- value of the connected pixelsnval
- value to propagatepublic void propagation6(int xx, int yy, int zz, int val, int nval)
xx
- x of the first pointyy
- y of the first pointzz
- z of the first pointval
- value of the connected pixelsnval
- value to propagatepublic void propagation(IntImage3D base, int abs, int ord, int prof, int val, int nval)
abs
- x of the first pointord
- y of the first pointprof
- z of the first pointval
- value of the connected pixelsnval
- value to propagatebase
- Description of the Parameterpublic IntImage3D watershed()
public ImageInt binaryReconstruct(ImageInt base)
base
- Description of the Parameterpublic IntImage3D grayReconstruction(IntImage3D base)
public IntImage3D RH_Maxima(int R, int H)
R
- Paramètre du rayon RH
- Paramètre de la hauteur Hpublic IntImage3D nbNeighbor(int obj)
obj
- Value of neighborhood pixels (including itself)public int nbConnexite2D(int val, int z)
z
- Description of the Parameterval
- Description of the Parameterprotected void propagation2D(int abs, int ord, int prof, int val, int nval)
abs
- Description of the Parameterord
- Description of the Parameterprof
- Description of the Parameterval
- Description of the Parameternval
- Description of the Parameterprotected IntImage3D projection(int val, int axe, int p1, int p2)
val
- Description of the Parameteraxe
- Description of the Parameterp1
- Description of the Parameterp2
- Description of the Parameterpublic IntImage3D projectionZ(int val)
val
- Description of the Parameterpublic IntImage3D projectionZ(int val, int p1, int p2)
val
- Description of the Parameterp1
- Description of the Parameterp2
- Description of the Parameterpublic IntImage3D projectionY(int val)
val
- Description of the Parameterpublic IntImage3D projectionX(int val)
val
- Description of the Parameterpublic int snr3D()
public IntImage3D sobelFilter()
public IntImage3D gradient(int axis)
axis
- x,y, or zpublic RealImage3D computeHessianDerivative(int value)
value
- (0=energy 1=coherence)public IntImage3D fillHoles3D(int background, int object)
background
- background levelobject
- gray level of object