edu.jhu.ece.iacl.algorithms.manual_label
Class LabelImage

java.lang.Object
  edu.jhu.ece.iacl.algorithms.manual_label.LabelImage

Direct Known Subclasses:

ROI

public class LabelImage
extends java.lang.Object

Field Summary

protected java.util.ArrayList<java.lang.Integer>	allComparisonHits
protected java.util.ArrayList<java.lang.Integer>	allhits
protected ImageData	img
protected java.lang.String	name
protected float	resX
protected float	resY
protected float	resZ
static java.lang.String	revnum
protected java.util.TreeSet<GridPt>	searched

Constructor Summary

LabelImage()

LabelImage(ImageData img)

LabelImage(java.util.List<ImageData> imgs)

Method Summary

double[][]	computeStatistics(LabelImage a) Computes a number of statistics between this LabelImage and another LabelImage {Dice Coefficient, Jaccard Coefficient, the containment of this object in A, the containment of A in this object, the Mountford Index, True Positive, True Negative, False Positive, and False Negative} for each label in this image.
static ImageData	discreteLabelsFromMemberships(java.util.List<ImageData> imgs, float thresh)
static ImageData	discreteLabelsFromMemberships(java.util.List<ImageData> imgs, java.util.List<java.lang.Integer> labellist, float thresh)
static double	fleissReliability(java.util.List<LabelImage> list)
static java.lang.String	get_version()
static java.util.ArrayList<java.lang.Integer>	getCombinedLabelList(java.util.List<LabelImage> list)
int[]	getDims()
int	getHitIndex(int hit)
ImageData	getImg()
XYZ	getlabCM(int lab)
static java.util.ArrayList<LabelImage>	getLabelImageList(java.util.List<ImageData> imglist)
java.util.ArrayList<java.lang.Integer>	getLabelList()
double	getLabelVolume(int lab)
java.util.ArrayList<GridPt>	getlabset(int lab)
GridPt[]	getlabsetArray(int lab)
java.util.ArrayList<java.lang.Integer>	getLastComparisonHits()
java.lang.String	getName()
int	getPt(GridPt pt)
int	getVal(GridPt p)
int	getVal(int x, int y, int z)
boolean	isinBounds(GridPt pt)
boolean	isPtinBounds(GridPt pt)
static boolean	isPtinBounds(int[][][] vol, GridPt pt)
double[]	meanDists(LabelImage a)
double	meanDists(LabelImage a, int label)
double[]	oneWayHausdorffDistance(LabelImage b, int lab)
LabelImage	organizeLabels()
static java.lang.String	runAllComparisons(java.util.List<ImageData> list, int numRaters)
static java.lang.String	runCenterOfMasses(java.util.List<ImageData> list, int label)
static java.lang.String	runCMDistance(java.util.List<ImageData> list, int numRaters, int label)
static java.lang.String[]	runHausdorfDistance(java.util.List<LabelImage> list, int label)
static java.lang.String	runMeanDistance(java.util.List<ImageData> list, int numRaters, int label)
static java.lang.String	runVolumes(java.util.List<ImageData> list, int label)
boolean	sameDims(LabelImage a)
java.util.HashMap<java.lang.Integer,ImageData>	separateLabels()
void	setimg(ImageData img)
void	setRes(float resX, float resY, float resZ)
void	setVal(int val, GridPt p)
void	setVal(int val, int x, int y, int z)
static LabelImage	unifyMasks(LabelImage[] imgs)

Methods inherited from class java.lang.Object

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

Field Detail

revnum

public static final java.lang.String revnum

img

protected ImageData img

allhits

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

allComparisonHits

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

searched

protected java.util.TreeSet<GridPt> searched

name

protected java.lang.String name

resX

protected float resX

resY

protected float resY

resZ

protected float resZ

Constructor Detail

LabelImage

public LabelImage()

LabelImage

public LabelImage(ImageData img)

LabelImage

public LabelImage(java.util.List<ImageData> imgs)

Method Detail

get_version

public static java.lang.String get_version()

setimg

public void setimg(ImageData img)

getImg

public ImageData getImg()

getName

public java.lang.String getName()

getPt

public int getPt(GridPt pt)

getVal

public int getVal(int x,
                  int y,
                  int z)

getVal

public int getVal(GridPt p)

setVal

public void setVal(int val,
                   int x,
                   int y,
                   int z)

setVal

public void setVal(int val,
                   GridPt p)

setRes

public void setRes(float resX,
                   float resY,
                   float resZ)

getDims

public int[] getDims()

getLastComparisonHits

public java.util.ArrayList<java.lang.Integer> getLastComparisonHits()

isPtinBounds

public boolean isPtinBounds(GridPt pt)

sameDims

public boolean sameDims(LabelImage a)

isPtinBounds

public static boolean isPtinBounds(int[][][] vol,
                                   GridPt pt)

getlabsetArray

public GridPt[] getlabsetArray(int lab)

getlabset

public java.util.ArrayList<GridPt> getlabset(int lab)

getLabelVolume

public double getLabelVolume(int lab)

getlabCM

public XYZ getlabCM(int lab)

unifyMasks

public static LabelImage unifyMasks(LabelImage[] imgs)

separateLabels

public java.util.HashMap<java.lang.Integer,ImageData> separateLabels()

isinBounds

public boolean isinBounds(GridPt pt)

getLabelList

public java.util.ArrayList<java.lang.Integer> getLabelList()

computeStatistics

public double[][] computeStatistics(LabelImage a)

Computes a number of statistics between this LabelImage and another LabelImage {Dice Coefficient, Jaccard Coefficient, the containment of this object in A, the containment of A in this object, the Mountford Index, True Positive, True Negative, False Positive, and False Negative} for each label in this image. Note for True Positive(TP), TN, FP and FN: this object is considered the truth.

Parameters:

a - a LabelImage to compare to this LabelImage

oneWayHausdorffDistance

public double[] oneWayHausdorffDistance(LabelImage b,
                                        int lab)

organizeLabels

public LabelImage organizeLabels()

getHitIndex

public int getHitIndex(int hit)

meanDists

public double[] meanDists(LabelImage a)

meanDists

public double meanDists(LabelImage a,
                        int label)

runAllComparisons

public static java.lang.String runAllComparisons(java.util.List<ImageData> list,
                                                 int numRaters)

fleissReliability

public static double fleissReliability(java.util.List<LabelImage> list)

getCombinedLabelList

public static java.util.ArrayList<java.lang.Integer> getCombinedLabelList(java.util.List<LabelImage> list)

getLabelImageList

public static java.util.ArrayList<LabelImage> getLabelImageList(java.util.List<ImageData> imglist)

runMeanDistance

public static java.lang.String runMeanDistance(java.util.List<ImageData> list,
                                               int numRaters,
                                               int label)

runCMDistance

public static java.lang.String runCMDistance(java.util.List<ImageData> list,
                                             int numRaters,
                                             int label)

runCenterOfMasses

public static java.lang.String runCenterOfMasses(java.util.List<ImageData> list,
                                                 int label)

runVolumes

public static java.lang.String runVolumes(java.util.List<ImageData> list,
                                          int label)

runHausdorfDistance

public static java.lang.String[] runHausdorfDistance(java.util.List<LabelImage> list,
                                                     int label)

discreteLabelsFromMemberships

public static ImageData discreteLabelsFromMemberships(java.util.List<ImageData> imgs,
                                                      float thresh)

discreteLabelsFromMemberships

public static ImageData discreteLabelsFromMemberships(java.util.List<ImageData> imgs,
                                                      java.util.List<java.lang.Integer> labellist,
                                                      float thresh)