@Deprecated
public abstract class Image3D
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
BYTE
Deprecated.
BYTE
|
protected float |
centerx
Deprecated.
center x of the image
|
protected float |
centery
Deprecated.
center y of the image
|
protected float |
centerz
Deprecated.
center z of the image
|
static int |
FLOAT
Deprecated.
FLOAT
|
protected ImageStack |
IJstack
Deprecated.
The ImageJ IJstack that stores the pixels data ( a 1D array could be more
efficient )
|
protected Voxel3D |
maxPixel
Deprecated.
where is the maxPixel pixel
|
protected float |
meanValue
Deprecated.
average value of the image
|
protected Voxel3D |
minPixel
Deprecated.
where is the minPixel pixel
|
protected boolean |
multithread
Deprecated.
|
static int |
SHORT
Deprecated.
SHORT
|
protected boolean |
showStatus
Deprecated.
|
protected int |
sizex
Deprecated.
size x
|
protected int |
sizey
Deprecated.
size y
|
protected int |
sizez
Deprecated.
size z
|
protected float |
stDev
Deprecated.
std dev of the image
|
int |
type
Deprecated.
type of data
|
static int |
XAXIS
Deprecated.
Axis X
|
static int |
YAXIS
Deprecated.
Axis Y
|
static int |
ZAXIS
Deprecated.
Axis Z
|
Constructor and Description |
---|
Image3D(ImageStack ijstack)
Deprecated.
Constructor for the Image3D object from a ImageJ IJstack
|
Image3D(int sizex,
int sizey,
int sizez,
int type)
Deprecated.
Constructor for the Image3D object
|
Modifier and Type | Method and Description |
---|---|
abstract IntImage3D |
binarisation(int threshLow,
int threshHigh)
Deprecated.
Thresholding, create a binarised image
|
protected void |
computeMinMax()
Deprecated.
compute the min and max pixels
|
static int[] |
createKernelEllipsoid(float radx,
float rady,
float radz)
Deprecated.
Create a kernel neighorhood as an ellipsoid
|
abstract Image3D |
createLocalMaximaImage(float radx,
float rady,
float radz,
boolean keep)
Deprecated.
Create a image with local maxima
|
Image3D |
crop(int newzerox,
int newzeroy,
int newzeroz,
int newsizex,
int newsizey,
int newsizez)
Deprecated.
Cropping of the image
|
double |
crossCorrelationNormalized(Image3D other,
int x0,
int y0,
int z0,
int x1,
int y1,
int z1,
int rx,
int ry,
int rz)
Deprecated.
Cross correlation between this image and another one at a specified
location .
|
Image3D |
extract(int x0,
int y0,
int z0,
int rx,
int ry,
int rz,
boolean sphere)
Deprecated.
Extract a 3D image from a specified location as the center of crop
|
float |
getCenterX()
Deprecated.
Gets the centerX attribute of the Image3D object
|
float |
getCenterY()
Deprecated.
Gets the centerY attribute of the Image3D object
|
float |
getCenterZ()
Deprecated.
Gets the centerZ attribute of the Image3D object
|
protected double |
getFloatMaximum()
Deprecated.
Gets the maximum pixel value
|
protected double |
getFloatMinimum()
Deprecated.
Gets the minimum pixel value
|
abstract HistogramUtil |
getHistogram()
Deprecated.
compute the histogram of the image
|
double[] |
getLinePixelValue(int x0,
int y0,
int z0,
int x1,
int y1,
int z1,
boolean interpolated)
Deprecated.
|
double[] |
getLinePixelValue(Point3D origin,
Vector3D dir,
double distNeg,
double distPos,
boolean interpolated)
Deprecated.
|
Voxel3D |
getMaxPixel()
Deprecated.
Gets the maxPixel attribute of the Image3D object
|
float |
getMean()
Deprecated.
Gets the mean Value of the Image3D
|
int |
getNbPixel()
Deprecated.
|
ArrayUtil |
getNeighborhood(Image3D ker,
int x,
int y,
int z)
Deprecated.
Gets the neighboring of a pixel, with a kernel as an image
|
ArrayUtil |
getNeighborhood(int x,
int y,
int z,
float radx,
float rady,
float radz)
Deprecated.
Gets the neighboring of a pixel (default=sphere)
|
ArrayUtil |
getNeighborhood3x3x3(int x,
int y,
int z)
Deprecated.
Gets the 3D neighborhood of the pixel in 8 connexion --> 27 pixels
|
ArrayUtil |
getNeighborhoodCross3D(int x,
int y,
int z)
Deprecated.
|
ArrayUtil |
getNeighborhoodGrayKernelAdd(IntImage3D ker,
int x,
int y,
int z)
Deprecated.
|
ArrayUtil |
getNeighborhoodGrayKernelMinus(IntImage3D ker,
int x,
int y,
int z)
Deprecated.
|
ArrayUtil |
getNeighborhoodKernel(int[] ker,
int nbval,
int x,
int y,
int z,
float radx,
float rady,
float radz)
Deprecated.
Gets the neighboring attribute of the Image3D with a kernel as a array
|
ArrayUtil |
getNeighborhoodLayer(int x,
int y,
int z,
float r0,
float r1)
Deprecated.
Get the neighborhood as a layer of pixels
|
ArrayUtil |
getNeighborhoodLayer(int x,
int y,
int z,
float r0,
float r1,
IntImage3D water)
Deprecated.
Get the neighborhood as a layer of pixels
|
ArrayUtil |
getNeighborhoodSphere(int x,
int y,
int z,
float radx,
float rady,
float radz)
Deprecated.
Gets the neighboring of a pixel (sphere)
|
ArrayUtil |
getNeighborhoodSphere(int x,
int y,
int z,
float radx,
float rady,
float radz,
RealImage3D edm)
Deprecated.
Gets the neighboring of a pixel (sphere)
|
abstract float |
getPix(float x,
float y,
float z)
Deprecated.
Gets the voxel value of the Image3D object (interpolated value)
|
abstract float |
getPix(int x,
int y,
int z)
Deprecated.
Gets the voxel value of the Image3D object
|
abstract float |
getPix(Voxel3D vox,
boolean b)
Deprecated.
|
ImagePlus |
getPlus()
Deprecated.
|
float |
getSigma()
Deprecated.
Gets the std dev value of the Image3D
|
int |
getSizex()
Deprecated.
Gets the sizex attribute of the Image3D object
|
int |
getSizey()
Deprecated.
Gets the sizey attribute of the Image3D object
|
int |
getSizez()
Deprecated.
Gets the sizez attribute of the Image3D object
|
ImageStack |
getStack()
Deprecated.
Get the imageJ IJstack (for displaying)
|
float |
getSumAbs()
Deprecated.
Gets the sum of absolute values of the Image3D
|
int |
getType()
Deprecated.
Gets the data type attribute of the Image3D object
|
void |
insert(Image3D vol,
int x0,
int y0,
int z0,
boolean average)
Deprecated.
Insert a 3D image to a specified location
|
void |
kill()
Deprecated.
Kill the Image3D
|
double[] |
radialDistribution(int x0,
int y0,
int z0,
int maxR)
Deprecated.
Radial distribution of pixels mean values in layers
|
double[] |
radialDistribution(int x0,
int y0,
int z0,
int maxR,
IntImage3D water)
Deprecated.
Radial distribution of pixels mean values in layers
|
void |
reset()
Deprecated.
set all pixels to 0
|
void |
reset(float nb)
Deprecated.
Reset the image to a given value
|
abstract void |
setPix(int x,
int y,
int z,
double value)
Deprecated.
Sets the voxel value
|
void |
setShowStatus(boolean showStatus)
Deprecated.
|
Image3D[] |
split(int axis,
int nb,
int overlap)
Deprecated.
Split a image into sub images
|
protected int sizex
protected int sizey
protected int sizez
public final int type
public static final int BYTE
public static final int SHORT
public static final int FLOAT
protected Voxel3D maxPixel
protected Voxel3D minPixel
protected float stDev
protected float meanValue
protected float centerx
protected float centery
protected float centerz
public static final int XAXIS
public static final int YAXIS
public static final int ZAXIS
protected ImageStack IJstack
protected boolean showStatus
protected boolean multithread
public Image3D(int sizex, int sizey, int sizez, int type)
sizex
- Size in x of the imagesizey
- Size in y of the imagesizez
- Size in z of the imagetype
- Data type in the imagepublic Image3D(ImageStack ijstack)
ijstack
- imageJ IJstackpublic void setShowStatus(boolean showStatus)
showStatus
- public void kill()
public void reset()
public void reset(float nb)
nb
- public ImageStack getStack()
public ImagePlus getPlus()
public abstract float getPix(int x, int y, int z)
x
- x coordinate of the voxely
- y coordinate of the voxelz
- z coordinate of the voxelpublic abstract float getPix(float x, float y, float z)
x
- x coordinate of the voxely
- y coordinate of the voxelz
- z coordinate of the voxelpublic abstract void setPix(int x, int y, int z, double value)
x
- x coordinate of the voxely
- y coordinate of the voxelz
- z coordinate of the voxelvalue
- The new voxel valuepublic double[] getLinePixelValue(int x0, int y0, int z0, int x1, int y1, int z1, boolean interpolated)
public double[] getLinePixelValue(Point3D origin, Vector3D dir, double distNeg, double distPos, boolean interpolated)
public int getSizex()
public int getSizey()
public int getSizez()
public int getNbPixel()
public int getType()
public float getCenterX()
public float getCenterY()
public float getCenterZ()
protected double getFloatMaximum()
protected double getFloatMinimum()
protected void computeMinMax()
public float getMean()
public float getSumAbs()
public float getSigma()
public Voxel3D getMaxPixel()
public double crossCorrelationNormalized(Image3D other, int x0, int y0, int z0, int x1, int y1, int z1, int rx, int ry, int rz)
other
- the other imagex0
- the x-coordinate in this imagey0
- the y-coordinate in this imagez0
- the z-coordinate in this imagex1
- the x-coordinate in other imagey1
- the x-coordinate in other imagez1
- the x-coordinate in other imagerx
- the radius x to compute correlationry
- the radius y to compute correlationrz
- the radius z to compute correlationpublic ArrayUtil getNeighborhoodSphere(int x, int y, int z, float radx, float rady, float radz)
x
- Coordinate x of the pixely
- Coordinate y of the pixelz
- Coordinate z of the pixelradx
- Radius x of the neighboringrady
- Radius y of the neighboringradz
- Radius z of the neighboringpublic ArrayUtil getNeighborhoodSphere(int x, int y, int z, float radx, float rady, float radz, RealImage3D edm)
x
- Coordinate x of the pixely
- Coordinate y of the pixelz
- Coordinate z of the pixelradx
- Radius x of the neighboringrady
- Radius y of the neighboringradz
- Radius z of the neighboringedm
- public ArrayUtil getNeighborhood3x3x3(int x, int y, int z)
x
- x coordinatey
- y coordinatez
- z coordinatepublic ArrayUtil getNeighborhoodCross3D(int x, int y, int z)
x
- y
- z
- public ArrayUtil getNeighborhood(int x, int y, int z, float radx, float rady, float radz)
x
- Coordinate x of the pixely
- Coordinate y of the pixelz
- Coordinate z of the pixelradx
- Radius x of the neighboringrady
- Radius y of the neighboringradz
- Radius z of the neighboringpublic ArrayUtil getNeighborhoodLayer(int x, int y, int z, float r0, float r1, IntImage3D water)
x
- Coordinate x of the pixely
- Coordinate y of the pixelz
- Coordinate z of the pixelr0
- Minimu radius valuer1
- Maximum radius valuewater
- public ArrayUtil getNeighborhoodLayer(int x, int y, int z, float r0, float r1)
x
- Coordinate x of the pixely
- Coordinate y of the pixelz
- Coordinate z of the pixelr0
- Minimu radius valuer1
- Maximum radius valuepublic double[] radialDistribution(int x0, int y0, int z0, int maxR, IntImage3D water)
x0
- Coordinate x of the pixely0
- Coordinate y of the pixelz0
- Coordinate z of the pixelmaxR
- maximu radiuswater
- public double[] radialDistribution(int x0, int y0, int z0, int maxR)
x0
- Coordinate x of the pixely0
- Coordinate y of the pixelz0
- Coordinate z of the pixelmaxR
- maximu radiuspublic ArrayUtil getNeighborhood(Image3D ker, int x, int y, int z)
x
- Coordinate x of the pixely
- Coordinate y of the pixelz
- Coordinate z of the pixelker
- The kernel (0 = outside kernel, else inside)public ArrayUtil getNeighborhoodKernel(int[] ker, int nbval, int x, int y, int z, float radx, float rady, float radz)
ker
- The kernel array (>0 ok)nbval
- The number of non-zero valuesx
- Coordinate x of the pixely
- Coordinate y of the pixelz
- Coordinate z of the pixelradx
- Radius x of the neighboringradz
- Radius y of the neighboringrady
- Radius z of the neighboringpublic ArrayUtil getNeighborhoodGrayKernelAdd(IntImage3D ker, int x, int y, int z)
ker
- x
- y
- z
- public ArrayUtil getNeighborhoodGrayKernelMinus(IntImage3D ker, int x, int y, int z)
ker
- x
- y
- z
- public static int[] createKernelEllipsoid(float radx, float rady, float radz)
radx
- Radius x of the ellipsoidrady
- Radius x of the ellipsoidradz
- Radius x of the ellipsoidpublic void insert(Image3D vol, int x0, int y0, int z0, boolean average)
vol
- the 3D image to be insertedx0
- the x coordinate of the insertiony0
- the y coordinate of the insertionz0
- the z coordinate of the insertionaverage
- average with original image or notpublic Image3D extract(int x0, int y0, int z0, int rx, int ry, int rz, boolean sphere)
x0
- the x coordinate of the center of the extractiony0
- the y coordinate of the center of the extractionz0
- the z coordinate of the center of the extractionrx
- radius X of new imagery
- radius Y of new imagerz
- radius Z of new imagesphere
- extract inside a spherepublic Image3D crop(int newzerox, int newzeroy, int newzeroz, int newsizex, int newsizey, int newsizez)
newzerox
- Start of the crop in xnewzeroy
- Start of the crop in xnewzeroz
- Start of the crop in znewsizex
- New size in xnewsizey
- New size in ynewsizez
- New size in zpublic Image3D[] split(int axis, int nb, int overlap)
axis
- The axis to split alongnb
- The number of splitted partsoverlap
- The overlap (in pixels)public abstract Image3D createLocalMaximaImage(float radx, float rady, float radz, boolean keep)
radx
- Radius in xrady
- Radius in yradz
- Radius in zkeep
- Keep original values of pixelspublic abstract IntImage3D binarisation(int threshLow, int threshHigh)
threshLow
- Low thresholdthreshHigh
- high thresholdpublic abstract HistogramUtil getHistogram()
public abstract float getPix(Voxel3D vox, boolean b)
vox
- the voxelb
- interpolated if true, rounded if false