mcib3d.image3d.legacy

Class RealImage3D

java.lang.Object

mcib3d.image3d.legacy.Image3D

mcib3d.image3d.legacy.RealImage3D

Direct Known Subclasses:

FHTImage3D

Deprecated.

@Deprecated
public class RealImage3D
extends Image3D

Description of the Class

Field Summary

Fields inherited from class mcib3d.image3d.legacy.Image3D

BYTE, centerx, centery, centerz, FLOAT, IJstack, maxPixel, meanValue, minPixel, multithread, SHORT, showStatus, sizex, sizey, sizez, stDev, type, XAXIS, YAXIS, ZAXIS

Constructor Summary

Constructors

Constructor and Description
RealImage3D(ImagePlus plus) Deprecated.
RealImage3D(ImageProcessor ip) Deprecated. Constructor for the RealImage3D object
RealImage3D(ImageStack pile) Deprecated. constructeur d'un volume a partir d'un IJstack
RealImage3D(int sizex, int sizey, int sizez) Deprecated. constructeur d'un volume vide (noir)
RealImage3D(int sizex, int sizey, int sizez, float[][] data) Deprecated. Constructor for the RealImage3D object

Method Summary

Modifier and Type	Method and Description
RealImage3D	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
RealImage3D	add(RealImage3D img) Deprecated. adds a RealImage3D to this one
RealImage3D	add(RealImage3D img, ArrayUtil transform) Deprecated. adds a transformed RealImage3D to this one
RealImage3D	add(RealImage3D img, GeomTransform3D transf) Deprecated. adds a transformed RealImage3D to this one
Image3D	addImage(Image3D img, float s, float t) Deprecated. Adds a feature to the Image attribute of the RealImage3D object
Image3D	addImage(RealImage3D img, float t) Deprecated. Adds a feature to the Image attribute of the RealImage3D object
RealImage3D	addValue(float value) Deprecated. adds a given value to all pixels
RealImage3D	applyTransform(GeomTransform3D trans) Deprecated. 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) Deprecated. Description of the Method
IntImage3D	binarisation(int seuilb, int seuilh) Deprecated. binarisation de l'image
RealImage3D	centerCrop(int newsizex, int newsizey, int newsizez) Deprecated. Description of the Method
RealImage3D	createLocalMaximaImage(float voisx, float voisy, float voisz, boolean keep) Deprecated. 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) Deprecated. Description of the Method
Image3D	dilatation3D(int fond, int voisx, int voisy, int voisz) Deprecated. base pour la morphologie mathématique binaire (dilatation) Les objets sont segmentes et ont donc une couleur différente du fond
RealImage3D	divideBy(float div) Deprecated. divides all pixels by a value
Image3D	erosion3D(int fond, int voisx, int voisy, int voisz) Deprecated. Description of the Method
Image3D	fermeture3D(int fond, int voisx, int voisy, int voisz, int ite) Deprecated. Description of the Method
void	filterGeneric(RealImage3D out, float radx, float rady, float radz, int zmin, int zmax, int filter) Deprecated. 3D filter using threads
HistogramUtil	getHistogram() Deprecated. 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() Deprecated. donne le maximum de l'image3D
double	getMinimum() Deprecated. donne le minimum de l'image3D
float	getPix(float x, float y, float z) Deprecated. Gets the trilinear interpolated pixel value at position (x,y,z) as a double
float	getPix(int x, int y, int z) Deprecated. Gets the pixel value at position (x,y,z) as a double
float	getPix(Voxel3D vox, boolean b) Deprecated.
float	getPixel(double x, double y, double z) Deprecated.
float	getPixel(float x, float y, float z) Deprecated. Gets the trilinear interpolated pixel value at position (x,y,z)
float	getPixel(int x, int y, int z) Deprecated. Gets the pixel value at position (x,y,z)
float	getPixelTransformedI(double X, double Y, double Z, GeomTransform3D inverttrans) Deprecated. Gets the pixel corresponding to the direct application of the transform given
float	getPixelTransformedI(Voxel3D pixel, GeomTransform3D inverttrans) Deprecated. Gets the pixel corresponding to the direct application of the transform given
RealImage3D	getPow2Img() Deprecated. Gets the pow2Img attribute of the RealImage3D object
RealImage3D	getPow2Img(int sizexmax, int sizeymax, int sizezmax) Deprecated. Gets the pow2Img attribute of the RealImage3D object
ImageStack	getStack() Deprecated. Gets the IJstack attribute of the RealImage3D object
float	getTransformPixel(Voxel3D pixel, GeomTransform3D trans) Deprecated. Gets the pixel corresponding to the pixel given if the transform is applied (inversion of matrice)
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
RealImage3D	maximumFilter(int voisx, int voisy, int voisz) Deprecated. filtre le volume grace a un filtre maximum 3D
Image3D	medianFilter(int voisx, int voisy, int voisz) Deprecated. filtre le volume grace a un filtre median 3D
Image3D	minimumFilter(int voisx, int voisy, int voisz) Deprecated. filtre le volume grace a un filtre minimum 3D
RealImage3D	multiplyBy(float mult) Deprecated. multiplies all pixels by a given value
RealImage3D	multiplyBy(Image3D mult) Deprecated.
Image3D	nonLinearLaplacianFilter(int voisx, int voisy, int voisz) Deprecated. filtre le volume grace a un filtre laplacien non lineaire
Image3D	ouverture3D(int fond, int voisx, int voisy, int voisz, int ite) Deprecated. Description of the Method
RealImage3D	project(int axis) Deprecated. Description of the Method
RealImage3D	project(Vector3D V, Vector3D C, boolean moy) Deprecated. Description of the Method
FloatProcessor	projection(Vector3D V, Vector3D C, boolean moy) Deprecated. Description of the Method
FloatProcessor	projectionInterpolated(Vector3D W, boolean moy) Deprecated. Projection by interpolation
void	putPixel(int x, int y, int z, double value) Deprecated. Description of the Method
void	putPixel(int x, int y, int z, float value) Deprecated. Sets the pixel value at position (x,y,z)
RealImage3D	resetImage() Deprecated. Description of the Method
void	setPix(int x, int y, int z, double value) Deprecated. Sets the pixel value at position (x,y,z) as a double
void	setSizes(int sx, int sy, int sz) Deprecated. Sets the sizes attribute of the RealImage3D object
Image3D	tophatFilter(int voisx, int voisy, int voisz) Deprecated. filtre le volume grace a un filtre top hat

Methods inherited from class mcib3d.image3d.legacy.Image3D

computeMinMax, createKernelEllipsoid, 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

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)

Deprecated.

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)

Deprecated.

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(ImageStack pile)

Deprecated.

constructeur d'un volume a partir d'un IJstack

Parameters:

pile - IJstack en entree

RealImage3D

public RealImage3D(ImagePlus plus)

Deprecated.

RealImage3D

public RealImage3D(ImageProcessor ip)

Deprecated.

Constructor for the RealImage3D object

Parameters:

ip - Description of the Parameter

Method Detail

setSizes

public void setSizes(int sx,
                     int sy,
                     int sz)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

Parameters:

x -

y -

z -

Returns:

setPix

public void setPix(int x,
                   int y,
                   int z,
                   double value)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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 ImageStack getStack()

Deprecated.

Gets the IJstack attribute of the RealImage3D object

Overrides:

getStack in class Image3D

Returns:

The IJstack value

getMaximum

public double getMaximum()

Deprecated.

donne le maximum de l'image3D

Returns:

la valeur maximum de l'image3D

getMinimum

public double getMinimum()

Deprecated.

donne le minimum de l'image3D

Returns:

la valeur minimum de l'image3D

getPow2Img

public RealImage3D getPow2Img()

Deprecated.

Gets the pow2Img attribute of the RealImage3D object

Returns:

The pow2Img value

getPow2Img

public RealImage3D getPow2Img(int sizexmax,
                              int sizeymax,
                              int sizezmax)

Deprecated.

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(float voisx,
                                          float voisy,
                                          float voisz,
                                          boolean keep)

Deprecated.

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,
                              float voisx,
                              float voisy,
                              float voisz)

Deprecated.

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)

Deprecated.

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 HistogramUtil getHistogram()

Deprecated.

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)

Deprecated.

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

filterGeneric

public void filterGeneric(RealImage3D out,
                          float radx,
                          float rady,
                          float radz,
                          int zmin,
                          int zmax,
                          int filter)

Deprecated.

3D filter using threads

Parameters:

out -

radx - Radius of mean filter in x

rady - Radius of mean filter in y

radz - Radius of mean filter in z

zmin -

filter -

zmax -

adaptiveFilter

public RealImage3D 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

Parameters:

radx -

radz -

rady -

Returns:

3D filtered image

addImage

public Image3D addImage(RealImage3D img,
                        float t)

Deprecated.

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)

Deprecated.

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,
                       ArrayUtil transform)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

Parameters:

mult -

Returns:

addValue

public RealImage3D addValue(float value)

Deprecated.

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)

Deprecated.

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)

Deprecated.

Description of the Method

Parameters:

trans - Description of the Parameter

Returns:

Description of the Return Value

getTransformPixel

public float getTransformPixel(Voxel3D pixel,
                               GeomTransform3D trans)

Deprecated.

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(Voxel3D pixel,
                                  GeomTransform3D inverttrans)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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()

Deprecated.

Description of the Method

Returns:

Description of the Return Value

medianFilter

public Image3D medianFilter(int voisx,
                            int voisy,
                            int voisz)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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 FloatProcessor projection(Vector3D V,
                                 Vector3D C,
                                 boolean moy)

Deprecated.

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 FloatProcessor projectionInterpolated(Vector3D W,
                                             boolean moy)

Deprecated.

Projection by interpolation

Parameters:

W - Direction of the projection

moy - Mean projection or sum

Returns:

Projected image

getPix

public float getPix(Voxel3D vox,
                    boolean b)

Deprecated.

Specified by:

getPix in class Image3D

Parameters:

vox -

b -

Returns: