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

java.lang.Object
  extended by edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
      extended by edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti

public class STAPLEmulti
extends AbstractCalculation


Field Summary
protected  int cols
           
protected  double convergesum
           
protected  java.lang.String dir
           
protected  double eps
           
protected  ImageDataInt hardseg
           
protected  java.util.List<ImageData> images
           
protected  int[][][][] imagesArray
           
protected  float[][][][] imagesArrayFloat
           
protected  java.lang.String initType
           
protected  java.util.ArrayList<java.lang.Integer> labels
           
protected  java.util.HashMap<java.lang.Integer,java.lang.Integer> labelstoindex
           
protected  int maxiters
           
protected  int MaxUniqueLabels
           
protected  java.lang.String mrfMethod
           
protected  float normtrace
           
protected  PerformanceLevel pl
           
protected  java.util.ArrayList<java.lang.Float> priors
           
protected  int raters
           
protected  int rows
           
protected  int slices
           
protected  java.util.ArrayList<ImageData> truth
           
protected  java.util.ArrayList<ImageData> truthclone
           
protected  float[][][][] truthImage
           
protected  int[][][][] uniqueLabels
           
 
Fields inherited from class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
monitor
 
Constructor Summary
STAPLEmulti()
           
STAPLEmulti(float[][][][] img)
           
STAPLEmulti(int[][][][] img)
           
STAPLEmulti(java.util.List<ImageData> img)
           
 
Method Summary
 void computeHardSeg()
           
 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()
           
 java.util.ArrayList<ImageData> getTruth()
           
 float[][][][] getTruthImage()
           
 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)
           
 boolean verifySizes()
           
 void writeHardSeg(java.io.File dir, java.lang.String name)
           
 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

imagesArray

protected int[][][][] imagesArray

imagesArrayFloat

protected float[][][][] imagesArrayFloat

images

protected java.util.List<ImageData> images

truthImage

protected float[][][][] truthImage

truth

protected java.util.ArrayList<ImageData> truth

truthclone

protected java.util.ArrayList<ImageData> truthclone

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

priors

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

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

mrfMethod

protected java.lang.String mrfMethod
Constructor Detail

STAPLEmulti

public STAPLEmulti()

STAPLEmulti

public STAPLEmulti(int[][][][] img)

STAPLEmulti

public STAPLEmulti(float[][][][] img)

STAPLEmulti

public STAPLEmulti(java.util.List<ImageData> 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)

verifySizes

public boolean verifySizes()

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()

iterate

public void iterate()

printPerformanceLevels

public void printPerformanceLevels()

getPerformanceLevels

public java.lang.String getPerformanceLevels()

getTruthImage

public float[][][][] getTruthImage()

getTruth

public java.util.ArrayList<ImageData> getTruth()

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)