edu.jhu.ece.iacl.algorithms.manual_label.staple
Class STAPLEmulti2

java.lang.Object
  edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
      edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2

public class STAPLEmulti2
extends AbstractCalculation

Field Summary

protected int	cols
protected double	convergesum
protected java.lang.String	dir
protected double	eps
protected ImageDataInt	hardseg
protected int[][][][]	imagesArray
protected float[][][][]	imagesArrayFloat
protected java.lang.String	initType
protected java.util.ArrayList<java.lang.Integer>	labels
protected int	labelSize
protected java.util.HashMap<java.lang.Integer,java.lang.Integer>	labelstoindex
protected int	maxiters
protected int	MaxUniqueLabels
protected boolean[][][][]	mindex
protected java.lang.String	mrfMethod
protected float	normtrace
protected PerformanceLevel	pl
protected PerformanceLevel	pl2
protected float[]	priorArray
protected java.util.ArrayList<java.lang.Float>	priors
protected int	raters
protected int	rows
protected int	slices
protected int[][][][]	t
protected long	te
protected long	tm
protected float[][][][]	truth
protected float[][][][]	truthclone
protected int	truthSize
protected int[][][][]	uniqueLabels

Fields inherited from class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation

monitor

Constructor Summary

STAPLEmulti2()

STAPLEmulti2(float[][][][] img)

STAPLEmulti2(int[][][][] img)

Method Summary

void	computeHardSeg()
void	createT()
void	distributeBeta()
void	Estep()
void	EstepEfficient()
void	findLabels()
ImageData	getHardSeg()
int[][][]	getHardSegArray()
int	getIndex(java.util.ArrayList<java.lang.Integer> l, java.lang.Integer n)
int	getIndex(int[] a, int n)
GridPt[]	getNeighbors(int i, int j, int k)
PerformanceLevel	getPeformanceLevel()
java.lang.String	getPerformanceLevels()
void	getPriorProb()
void	initialize()
void	iterate()
void	Mstep()
void	MstepEfficient()
void	printPerformanceLevels()
void	setBeta(float beta)
void	setConnectivity(GridPt.Connectivity c)
void	setDir(java.lang.String dir)
void	setEps(double eps)
void	setImages(int[][][][] img)
void	setInit(java.lang.String init)
void	setmaxIters(int max)
void	Step()
void	writeHardSeg(java.io.File dir, java.lang.String name)
java.util.ArrayList<ImageData>	writeProb(CubicVolumeCropper cropper)
void	writeTruth(java.io.File dir)
void	writeTruth(java.io.File dir, java.lang.String name)
void	writeUniqueLabels(java.io.File dir)

Methods inherited from class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation

add, addTotalUnits, decrementCompletedUnits, decrementCompletedUnits, getCompletedUnits, getCurrentLabel, getCurrentProgress, getLabel, getPerformance, getProgress, getTotalUnits, incrementCompletedUnits, incrementCompletedUnits, isCompleted, markCompleted, reset, setCompletedUnits, setCompletedUnits, setLabel, setMonitor, setTotalUnits

Methods inherited from class java.lang.Object

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

Field Detail

te

protected long te

tm

protected long tm

imagesArray

protected int[][][][] imagesArray

imagesArrayFloat

protected float[][][][] imagesArrayFloat

truth

protected float[][][][] truth

truthclone

protected float[][][][] truthclone

t

protected int[][][][] t

mindex

protected boolean[][][][] mindex

hardseg

protected ImageDataInt hardseg

MaxUniqueLabels

protected int MaxUniqueLabels

uniqueLabels

protected int[][][][] uniqueLabels

labelstoindex

protected java.util.HashMap<java.lang.Integer,java.lang.Integer> labelstoindex

pl

protected PerformanceLevel pl

pl2

protected PerformanceLevel pl2

priors

protected java.util.ArrayList<java.lang.Float> priors

priorArray

protected float[] priorArray

labels

protected java.util.ArrayList<java.lang.Integer> labels

convergesum

protected double convergesum

normtrace

protected float normtrace

maxiters

protected int maxiters

dir

protected java.lang.String dir

eps

protected double eps

initType

protected java.lang.String initType

rows

protected int rows

cols

protected int cols

slices

protected int slices

raters

protected int raters

labelSize

protected int labelSize

truthSize

protected int truthSize

mrfMethod

protected java.lang.String mrfMethod

Constructor Detail

STAPLEmulti2

public STAPLEmulti2()

STAPLEmulti2

public STAPLEmulti2(int[][][][] img)

STAPLEmulti2

public STAPLEmulti2(float[][][][] img)

Method Detail

setmaxIters

public void setmaxIters(int max)

setEps

public void setEps(double eps)

setImages

public void setImages(int[][][][] img)

setDir

public void setDir(java.lang.String dir)

setInit

public void setInit(java.lang.String init)

setBeta

public void setBeta(float beta)

distributeBeta

public void distributeBeta()

setConnectivity

public void setConnectivity(GridPt.Connectivity c)

getNeighbors

public GridPt[] getNeighbors(int i,
                             int j,
                             int k)

findLabels

public void findLabels()

initialize

public void initialize()

EstepEfficient

public void EstepEfficient()

Estep

public void Estep()

MstepEfficient

public void MstepEfficient()

Mstep

public void Mstep()

getPriorProb

public void getPriorProb()

createT

public void createT()

Step

public void Step()

iterate

public void iterate()

printPerformanceLevels

public void printPerformanceLevels()

getPerformanceLevels

public java.lang.String getPerformanceLevels()

writeProb

public java.util.ArrayList<ImageData> writeProb(CubicVolumeCropper cropper)

getPeformanceLevel

public PerformanceLevel getPeformanceLevel()

getIndex

public int getIndex(java.util.ArrayList<java.lang.Integer> l,
                    java.lang.Integer n)

getIndex

public int getIndex(int[] a,
                    int n)

getHardSeg

public ImageData getHardSeg()

computeHardSeg

public void computeHardSeg()

getHardSegArray

public int[][][] getHardSegArray()

writeTruth

public void writeTruth(java.io.File dir)

writeTruth

public void writeTruth(java.io.File dir,
                       java.lang.String name)

writeUniqueLabels

public void writeUniqueLabels(java.io.File dir)

writeHardSeg

public void writeHardSeg(java.io.File dir,
                         java.lang.String name)