mcib3d.image3d

Class Segment3DSpots

java.lang.Object

mcib3d.image3d.Segment3DSpots

public class Segment3DSpots
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
boolean	bigLabel
static int	LOCAL_CONSTANT
static int	LOCAL_DIFF
static int	LOCAL_GAUSS
static int	LOCAL_MEAN
boolean	multithread
static int	SEG_BLOCK
static int	SEG_CLASSICAL
static int	SEG_MAX
boolean	show

Constructor Summary

Constructors

Constructor and Description
Segment3DSpots(ImageHandler image, ImageHandler seeds)

Method Summary

Modifier and Type	Method and Description
double[]	gaussianFit(int x, int y, int z, boolean plotb)
ImageHandler	getInternalLabelImage()
ImageHandler	getLabelImage()
Voxel3D	getLocalMaximum(int x, int y, int z, float radx, float rady, float radz)
int	getLocalThreshold()
java.util.ArrayList<Object3D>	getObjects()
ImageHandler	getRawImage()
ImageHandler	getSeeds()
int	getSeedsThreshold()
int	getVolumeMax()
int	getVolumeMin()
double	localMean(int xc, int yc, int zc) Local mean for segmentation
void	segmentAll()
java.util.LinkedList<Voxel3D>	segmentOneSpot(int x, int y, int z, int o)
java.util.LinkedList<Voxel3D>	segmentSpotBlock(int xdep, int ydep, int zdep, int lcThreshold, int val)
java.util.LinkedList<Voxel3D>	segmentSpotClassical(int xdep, int ydep, int zdep, int lcThreshold, int val) Segment an object from a seed
java.util.LinkedList<Voxel3D>	segmentSpotMax(int xdep, int ydep, int zdep, int lcThreshold, int val) Segment an object from a seed, keep only max local
void	setGaussMaxr(int gm)
void	setGaussPc(double pc)
void	setLabelImage(ImageHandler image)
void	setLocalDiff(int d)
void	setLocalThreshold(int localThreshold)
void	setMethodLocal(int method)
void	setMethodSeg(int method)
void	setNoiseWatershed(int noiseWatershed) Deprecated.
void	setRadiusLocalMean(float r0, float r1, float r2)
void	setRadiusLocalMean(float r0, float r1, float r2, double we)
void	setRawImage(ImageHandler image)
void	setSeeds(ImageInt seeds)
void	setSeedsThreshold(int globalThreshold)
void	setVolumeMax(int volMax)
void	setVolumeMin(int volMin)
void	setWatershed(boolean wa)
static java.util.ArrayList<Voxel3D>[]	splitSpotProjection(IntImage3D ori, int val, Object3D f, int new1, int new2, double dist, float rad, int dim) NOT USED, see splitSpotWatershed
static Object3DVoxels[]	splitSpotWatershed(Object3D obj, float rad, float dist)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SEG_CLASSICAL

public static final int SEG_CLASSICAL

See Also:

Constant Field Values

SEG_MAX

public static final int SEG_MAX

See Also:

Constant Field Values

SEG_BLOCK

public static final int SEG_BLOCK

See Also:

Constant Field Values

LOCAL_CONSTANT

public static final int LOCAL_CONSTANT

See Also:

Constant Field Values

LOCAL_MEAN

public static final int LOCAL_MEAN

See Also:

Constant Field Values

LOCAL_GAUSS

public static final int LOCAL_GAUSS

See Also:

Constant Field Values

LOCAL_DIFF

public static final int LOCAL_DIFF

See Also:

Constant Field Values

show

public boolean show

multithread

public boolean multithread

bigLabel

public boolean bigLabel

Constructor Detail

Segment3DSpots

public Segment3DSpots(ImageHandler image,
                      ImageHandler seeds)

Parameters:

image - raw image

seeds - seeds image

Method Detail

splitSpotWatershed

public static Object3DVoxels[] splitSpotWatershed(Object3D obj,
                                                  float rad,
                                                  float dist)

splitSpotProjection

public static java.util.ArrayList<Voxel3D>[] splitSpotProjection(IntImage3D ori,
                                                                 int val,
                                                                 Object3D f,
                                                                 int new1,
                                                                 int new2,
                                                                 double dist,
                                                                 float rad,
                                                                 int dim)

NOT USED, see splitSpotWatershed

Parameters:

ori -

val -

f -

new1 -

new2 -

dist -

rad -

dim -

Returns:

getLocalThreshold

public int getLocalThreshold()

Returns:

current local threshold

setLocalThreshold

public void setLocalThreshold(int localThreshold)

Parameters:

localThreshold -

getSeedsThreshold

public int getSeedsThreshold()

Returns:

global threshold

setSeedsThreshold

public void setSeedsThreshold(int globalThreshold)

Parameters:

globalThreshold -

getRawImage

public ImageHandler getRawImage()

Returns:

raw image

setRawImage

public void setRawImage(ImageHandler image)

Parameters:

image -

getSeeds

public ImageHandler getSeeds()

Returns:

seeds image

setSeeds

public void setSeeds(ImageInt seeds)

Parameters:

seeds - image

getObjects

public java.util.ArrayList<Object3D> getObjects()

Returns:

getInternalLabelImage

public ImageHandler getInternalLabelImage()

Returns:

getLabelImage

public ImageHandler getLabelImage()

setLabelImage

public void setLabelImage(ImageHandler image)

setMethodSeg

public void setMethodSeg(int method)

Parameters:

method -

setMethodLocal

public void setMethodLocal(int method)

Parameters:

method -

setWatershed

public void setWatershed(boolean wa)

Parameters:

wa -

setNoiseWatershed

@Deprecated
public void setNoiseWatershed(int noiseWatershed)

Deprecated.

Parameters:

noiseWatershed -

setRadiusLocalMean

public void setRadiusLocalMean(float r0,
                               float r1,
                               float r2)

Parameters:

r0 -

r1 -

r2 -

setLocalDiff

public void setLocalDiff(int d)

setRadiusLocalMean

public void setRadiusLocalMean(float r0,
                               float r1,
                               float r2,
                               double we)

Parameters:

r0 -

r1 -

r2 -

we -

setGaussPc

public void setGaussPc(double pc)

Parameters:

pc -

setGaussMaxr

public void setGaussMaxr(int gm)

Parameters:

gm -

getVolumeMax

public int getVolumeMax()

Returns:

setVolumeMax

public void setVolumeMax(int volMax)

Parameters:

volMax -

getVolumeMin

public int getVolumeMin()

Returns:

setVolumeMin

public void setVolumeMin(int volMin)

Parameters:

volMin -

localMean

public double localMean(int xc,
                        int yc,
                        int zc)

Local mean for segmentation

Parameters:

xc - x coordinate of pixel

yc - y coordinate of pixel

zc - z coordinate of pixel

Returns:

the local mean at this position

gaussianFit

public double[] gaussianFit(int x,
                            int y,
                            int z,
                            boolean plotb)

Parameters:

x -

y -

z -

plotb -

Returns:

segmentAll

public void segmentAll()

segmentOneSpot

public java.util.LinkedList<Voxel3D> segmentOneSpot(int x,
                                                    int y,
                                                    int z,
                                                    int o)

segmentSpotBlock

public java.util.LinkedList<Voxel3D> segmentSpotBlock(int xdep,
                                                      int ydep,
                                                      int zdep,
                                                      int lcThreshold,
                                                      int val)

Parameters:

xdep -

ydep -

zdep -

lcThreshold -

val -

Returns:

segmentSpotClassical

public java.util.LinkedList<Voxel3D> segmentSpotClassical(int xdep,
                                                          int ydep,
                                                          int zdep,
                                                          int lcThreshold,
                                                          int val)

Segment an object from a seed

Parameters:

lcThreshold - Threshold to connect pixels

val - value of the object

xdep - x coordinate of the seed

ydep - y coordinate of the seed

zdep - z coordinate of the seed

Returns:

true if object cold be segmented

segmentSpotMax

public java.util.LinkedList<Voxel3D> segmentSpotMax(int xdep,
                                                    int ydep,
                                                    int zdep,
                                                    int lcThreshold,
                                                    int val)

Segment an object from a seed, keep only max local

Parameters:

lcThreshold - Threshold to connect pixels

val - value of the object

xdep - x coordinate of the seed

ydep - y coordinate of the seed

zdep - z coordinate of the seed

Returns:

true if object cold be segmented

getLocalMaximum

public Voxel3D getLocalMaximum(int x,
                               int y,
                               int z,
                               float radx,
                               float rady,
                               float radz)