A B C D E F G H I J K L M N O P R S T U V W X Y Z

A

abs(Complex) - Static method in class woSource.math.Complex

abs() - Method in class woSource.math.Complex

abs(double) - Static method in class woSource.math.MathI

shorthand for Math functions

abs(float) - Static method in class woSource.math.MathI

abs(int) - Static method in class woSource.math.MathI

absGradient - Static variable in class woSource.InteractiveSnake

accept(File, String) - Method in class woSource.math.woEndsWithFilter

acos() - Method in class woSource.math.Complex

acos(Complex) - Static method in class woSource.math.Complex

acos(double) - Static method in class woSource.math.MathI

05/24/2013 this version checks for round-off error in x; i.e.

acos(float) - Static method in class woSource.math.MathI

05/24/2013 this version checks for round-off error in x; i.e.

acosh() - Method in class woSource.math.Complex

acosh(Complex) - Static method in class woSource.math.Complex

acosh(double) - Static method in class woSource.math.MathI

acosh(float) - Static method in class woSource.math.MathI

acot() - Method in class woSource.math.Complex

acot(Complex) - Static method in class woSource.math.Complex

acoth() - Method in class woSource.math.Complex

acoth(Complex) - Static method in class woSource.math.Complex

acoth(double) - Static method in class woSource.math.MathI

acovers() - Method in class woSource.math.Complex

acovers(Complex) - Static method in class woSource.math.Complex

acqTime - Variable in class woSource.math.Image3Dinfo

acsc() - Method in class woSource.math.Complex

acsc(Complex) - Static method in class woSource.math.Complex

acsch() - Method in class woSource.math.Complex

acsch(Complex) - Static method in class woSource.math.Complex

acsch(double) - Static method in class woSource.math.MathI

actionPerformed(ActionEvent) - Method in class woSource.GenericRecallableDialog

addAndDisplay() - Method in class woSource.ImageOverlay

addAndDisplayInColor() - Method in class woSource.ImageOverlay

addBranch(int, int) - Method in class woSource.math.VesselTree

addBranchAndChildren(int, VesselTree, int) - Method in class woSource.math.VesselTree

WO 11/20/2012 Add the branch from a separate vessel tree (OrigVT) with it's index 'origIndexAt' as a new child of this tree's branch parentBr, and its decendants recursively.

addButton(String) - Method in class woSource.GenericRecallableDialog

Adds a button to the dialog window

addButton(String, int) - Method in class woSource.GenericRecallableDialog

addButtons(String, String) - Method in class woSource.GenericRecallableDialog

adds 2(3,4) buttons in a row to the dialog window.

addButtons(String, String, String) - Method in class woSource.GenericRecallableDialog

addButtons(String, String, String, String) - Method in class woSource.GenericRecallableDialog

addButtons(String, String, String, String, String) - Method in class woSource.GenericRecallableDialog

addButtonToPanel(String, Panel, GridBagLayout, int) - Method in class woSource.GenericRecallableDialog

addCanvas(Canvas) - Method in class woSource.GenericRecallableDialog

addCanvas(Canvas, int) - Method in class woSource.GenericRecallableDialog

addChild(int) - Method in class woSource.math.VesselBranch

addChoice(String, int, String) - Method in class woSource.GenericRecallableDialog

addChoice(String, int, String, int) - Method in class woSource.GenericRecallableDialog

addChoice(String, String[], String, int) - Method in class woSource.GenericRecallableDialog

addHalfBlock(float[][][], float[]) - Static method in class woSource.math.ImgProc

WO 8/6/2012 intent is to create a volume where the back half of the pixels are On, from point passing through the center and oriented by surface normal.

addHalfBlock4ptNormal(float[][][][], float[]) - Method in class woSource.noduleDetectionModule

addLandmark(Point3D) - Method in class woSource.Point3Dviewer

addLandmark(float[]) - Method in class woSource.Point3Dviewer

AddLoopLocIfUnique(int, int, int, int, int) - Method in class woSource.VesselSegm

xto, yto, zto is first point on looped-to branch

addOrphanedBranchLastPt(int, int) - Method in class woSource.VesselSegm

addOrphanedBranchPt(int, int) - Method in class woSource.VesselSegm

addPoint(float, float) - Method in class woSource.math.Polygon2D

addPoint(float, float, float) - Method in class woSource.math.Polygon3D

addPoint(int, int, int) - Method in class woSource.math.Polygon3Dint

addPt(Point2D) - Method in class woSource.InteractiveSnake.Snake

returns true if point added.

addPt(Point2D) - Method in class woSource.InteractiveSnake.SnakeStack

addPt(int, int, int, float) - Method in class woSource.math.VesselBranch

addPt(Point3Dint) - Method in class woSource.math.VesselBranch

addWall2Template(float[][][], NoduleCandidate, float) - Method in class woSource.LIDCreview

addWall2Template(float[][][], float, float, float, float) - Method in class woSource.LIDCreview

addWall2Template(float[][][][], NoduleCandidate, float) - Method in class woSource.LIDCreview

addWall2Template(float[][][][], float, float, float, float) - Method in class woSource.LIDCreview

adjustBranchRadii() - Method in class woSource.VesselSegm

set Branch average radii, correcting for skeleton points that intersect parent/child vessel.

adjustCurSlice() - Method in class woSource.ImageReviewer

adjustedDiff - Variable in class woSource.VesselSegm

adjustedMax - Variable in class woSource.AirwaySegm

adjustedMax - Variable in class woSource.PulmonaryTrunkSegm

adjustedMin - Variable in class woSource.PulmonaryTrunkSegm

adjustedMin - Variable in class woSource.VesselSegm

adjustNodalParam(int, int, int, float) - Method in class woSource.math.VesselTree

change the nodal param and recompute the smooth points that the sim image is based on.

adjustPt(int, Point2D, boolean) - Method in class woSource.InteractiveSnake.Snake

adjustPt(int, Point2D, boolean, boolean) - Method in class woSource.InteractiveSnake.Snake

adjustPt(int, Point2D, boolean, boolean) - Method in class woSource.InteractiveSnake.SnakeStack

aexsec() - Method in class woSource.math.Complex

aexsec(Complex) - Static method in class woSource.math.Complex

ahav() - Method in class woSource.math.Complex

ahav(Complex) - Static method in class woSource.math.Complex

airBGThresh - Variable in class woSource.PulmonaryTrunkSegm

airBGThresh_adjusted - Variable in class woSource.PulmonaryTrunkSegm

airwayMask - Variable in class woSource.VesselSegm

AirwaySegm - Class in woSource

AirwaySegm by W.

AirwaySegm() - Constructor for class woSource.AirwaySegm

allCoeffsToString() - Method in class woSource.ImageRegistrationPS

alpha - Variable in class woSource.math.ArrayDisplay

alreadyBodyCropped - Variable in class woSource.humanLungSegm

alreadyCropped - Variable in class woSource.humanLungSegm

alreadySavedParams - Variable in class woSource.ImageRegistration

amoeba(float[][], float[], float, int) - Method in class woSource.math.OptMath

amoeba_opt(float[]) - Method in class woSource.math.OptMath

amoeba_opt(float[], int) - Method in class woSource.math.OptMath

AND(boolean[][], boolean[][]) - Static method in class woSource.math.ArraysI

AND(boolean[][][], boolean[][][]) - Static method in class woSource.math.ArraysI

AND(byte[][][], boolean[][][]) - Static method in class woSource.math.ArraysI

WO 9/24/2013 want to combine a binary image of skeleton to original short image of chest CT

AND(short[][][], boolean[][][]) - Static method in class woSource.math.ArraysI

apicalFocalPt - Variable in class woSource.math.HeartLongAxis

append(LIDCnodule[], LIDCnodule[]) - Static method in class woSource.math.ArraysI

public static int[] sortLow2HighInsert(int[] A, int newval) { int i=0; // using '>=' to reduce amount of shifting to be done on insert while (i=A[i] && A[i]< Integer.MAX_VALUE) i++; if (i

append(LIDCnodule[], LIDCnodule[], LIDCnodule[]) - Static method in class woSource.math.ArraysI

merge such that result may be longer than either inputs

applyMask(byte[][], byte[][]) - Static method in class woSource.math.ImgProc

assumes you have binary mask with either 0 'OFF' or some value >0, meaning 'ON'

applyMask(byte[][], byte[][], byte) - Static method in class woSource.math.ImgProc

applyMask(short[][], byte[][]) - Static method in class woSource.math.ImgProc

applyMask(short[][], byte[][], short) - Static method in class woSource.math.ImgProc

applyMask(short[][], boolean[][]) - Static method in class woSource.math.ImgProc

applyMask(short[][], boolean[][], short) - Static method in class woSource.math.ImgProc

applyMask(float[][], byte[][]) - Static method in class woSource.math.ImgProc

applyMask(float[][], byte[][], float) - Static method in class woSource.math.ImgProc

applyMask(byte[][][], boolean[][][]) - Static method in class woSource.math.ImgProc

applyMask(byte[][][], byte[][][]) - Static method in class woSource.math.ImgProc

applyMask(short[][][], boolean[][][]) - Static method in class woSource.math.ImgProc

applyMask(short[][][], boolean[][][], short) - Static method in class woSource.math.ImgProc

WO 9/24/07 added this to fill DICOM CT images with -1000 instead of Min(A)

applyMask(short[][][], byte[][][]) - Static method in class woSource.math.ImgProc

applyMask(short[][][], byte[][][], short) - Static method in class woSource.math.ImgProc

WO 9/24/07 added this to fill DICOM CT images with -1000 instead of Min(A)

applySelectionTemplates() - Method in class woSource.noduleDetectionModule

applyTaggedFecesThresh() - Method in class woSource.ColonSegm

applyTemplates() - Method in class woSource.LIDCreview

applyTemplates() - Method in class woSource.noduleDetection

applyTemplates() - Method in class woSource.noduleDetectionModule

applyTemplates4Selections(int, int) - Method in class woSource.noduleDetectionModule

applyTemplates4Selections(int, int, int) - Method in class woSource.noduleDetectionModule

applyVertLineSegm() - Method in class woSource.ColonSegm

ApplyWiener3D() - Method in class woSource.Deconvolver

area() - Method in class woSource.math.Polygon2D

areaIntegral(float, float) - Static method in class woSource.math.MathII

WO 5/9/02 area under an arc: arc eqn: y^2 = sqrt(R^2 - x^2) area = integral{ sqrt(R^2 - x^2) dx}

areBranchesPaired(int, int, boolean, int, int, boolean) - Method in class woSource.VesselSegm

goal to test whether these 2 branches have similar trajectories and radii to indicate that they are really the same branch that has been interrupted by a crossing branch.

areBranchesPaired(VesselBranch, boolean, VesselBranch, boolean) - Method in class woSource.VesselSegm

areRadiiMatched(int, int, int, int) - Method in class woSource.VesselSegm

areRadiiMatched(VesselBranch, VesselBranch) - Method in class woSource.VesselSegm

arg(Complex) - Static method in class woSource.math.Complex

arg() - Method in class woSource.math.Complex

argDeg(Complex) - Static method in class woSource.math.Complex

argDeg() - Method in class woSource.math.Complex

argRad(Complex) - Static method in class woSource.math.Complex

argRad() - Method in class woSource.math.Complex

array1DToBitMask(int[][]) - Static method in class woSource.math.ArraysI

this maps a list of x,y coords of ON pixels into a 2D bit mask/image image dims passed as first entry in 1D array

ArrayColorDisplay - Class in woSource.math

WO started 4/21-22/08, latest edits/features 1/2013
ArrayColorDisplay creates internally an RGB image, rather than merely a grayscale image as with ArrayDisplay.
ACD uses ColorProcessors that store RGB values as 3 byte values, thus the grayscale image needs to be scaled 0..255.
This is used, for example, for image overlays within image registration software; and 3D rendering of vessels with different shaded colors for each vessel tree.

ArrayColorDisplay(byte[][]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][], String) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][], String, Properties) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][], String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][], String, String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

WO 1/30/2013 single slice byte[][] version.

ArrayColorDisplay(byte[][][]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][][], String) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][][], String, Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][][], int) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][][], String[], Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][][], String, String[], Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][][], String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][][], String, String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(byte[][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

WO 1/30/2013 image stack byte[][][] version.

ArrayColorDisplay(short[][]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][], String) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][], String, Properties) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][], String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][], String, String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][], String, Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][], String) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][], int) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][], String[], Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][], String, String[], Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][], String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][], String, String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][], String, String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(short[][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][], String) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][], String, Properties) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][], String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][], String, String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][], String, Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][], String) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][], int) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][], String[], Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][], String, String[], Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][], String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][], String, String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][][], String, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

4D is meant for diffusion tensor portrayal of direction of principle eigen vector the 4th array dim contains the 3 vector components of the eigen vector, which will be represented in the RG&B components

ArrayColorDisplay(float[][][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][][], String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][][], String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][][], String, Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][][], String[], Properties[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][][], String) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][][], String[]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][][]) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay(float[][][][], int) - Constructor for class woSource.math.ArrayColorDisplay

ArrayColorDisplay3D - Class in woSource.math

ACD3D handles having 3 windows open simultaneously and cooperatively.

ArrayColorDisplay3D(byte[][][], String) - Constructor for class woSource.math.ArrayColorDisplay3D

ArrayColorDisplay3D(byte[][][], String, Properties[]) - Constructor for class woSource.math.ArrayColorDisplay3D

ArrayColorDisplay3D(byte[][][], String, Properties[], Rectangle3D) - Constructor for class woSource.math.ArrayColorDisplay3D

ArrayColorDisplay3D(byte[][][], String, Properties[], Rectangle3D, int, int) - Constructor for class woSource.math.ArrayColorDisplay3D

ArrayColorDisplay3D(short[][][], String) - Constructor for class woSource.math.ArrayColorDisplay3D

ArrayColorDisplay3D(short[][][], String, Properties[]) - Constructor for class woSource.math.ArrayColorDisplay3D

ArrayColorDisplay3D(short[][][], String, Properties[], Rectangle3D) - Constructor for class woSource.math.ArrayColorDisplay3D

ArrayColorDisplay3D(short[][][], String, Properties[], Rectangle3D, int, int) - Constructor for class woSource.math.ArrayColorDisplay3D

ArrayDisplay - Class in woSource.math

ArrayDisplay is meant to take the hassle out of creating a window to display 2D and 3D (and 4D) data by handling all the windows variables (graphics, canvas, display, processors) automatically so the user does not have to know about these aspects.

ArrayDisplay() - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(ArrayDisplay) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(String, ArrayDisplay) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(ImagePlus, String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(ImagePlus, String, String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][], String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][], String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][], String, String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][], String, String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][], String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][], String, String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][], String, String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

permits multiple labels, one per slice

ArrayDisplay(boolean[][][], String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(boolean[][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(byte[][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][], String, String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][], String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][], String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][], String, String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(short[][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][], String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][], String, String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(int[][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][], String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][], String, String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][], String, String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(float[][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][], String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][], String, String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, String[], Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, String[], Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, String[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, String[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(double[][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][], String, Properties) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][], String, String, Properties, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][][], String) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][][], String, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][][], String, int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][][], String, int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][][], String, int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][][], String, int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][][], String[], int) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][][], String[], int, ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][][], String[], int, Properties[]) - Constructor for class woSource.math.ArrayDisplay

ArrayDisplay(Point3D[][][], String, String[], int, Properties[], ScreenSelectorClass) - Constructor for class woSource.math.ArrayDisplay

ArrayPlot - Class in woSource.math

ArrayPlot(int[]) - Constructor for class woSource.math.ArrayPlot

ArrayPlot(String, String, String, int[]) - Constructor for class woSource.math.ArrayPlot

ArrayPlot(float[]) - Constructor for class woSource.math.ArrayPlot

ArrayPlot(String, String, String, float[]) - Constructor for class woSource.math.ArrayPlot

ArrayPlot(String, String, String, float[], float[]) - Constructor for class woSource.math.ArrayPlot

ArrayPlot(String, String, String, float[], float, float) - Constructor for class woSource.math.ArrayPlot

ArrayPlot(String, String, String, float[], int) - Constructor for class woSource.math.ArrayPlot

ArraysI - Class in woSource.math

ArraysI contains manhy of my own functions that process 2D and 3D arrays

ArraysI() - Constructor for class woSource.math.ArraysI

ARSeedx - Variable in class woSource.PulmonaryTrunkSegm

ARSeedy - Variable in class woSource.PulmonaryTrunkSegm

ARSeedz - Variable in class woSource.PulmonaryTrunkSegm

asec() - Method in class woSource.math.Complex

asec(Complex) - Static method in class woSource.math.Complex

asech() - Method in class woSource.math.Complex

asech(Complex) - Static method in class woSource.math.Complex

asech(double) - Static method in class woSource.math.MathI

asin() - Method in class woSource.math.Complex

asin(Complex) - Static method in class woSource.math.Complex

asin(double) - Static method in class woSource.math.MathI

asin(float) - Static method in class woSource.math.MathI

asinh() - Method in class woSource.math.Complex

asinh(Complex) - Static method in class woSource.math.Complex

asinh(double) - Static method in class woSource.math.MathI

asinh(float) - Static method in class woSource.math.MathI

assocLegendre(int, int, double) - Static method in class woSource.math.MathII

from http://www.shodor.org/refdesk/Resources/Libraries/AssocLegendre/AssocLegendre.java
their on-line code had errors, but his below gives the correct results.

aStatsCorrCirc(short[][][], float[][][][], boolean, boolean[][][], int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

WO 2/15/11 added check whether at any image pixel, the overlapping kernel extends over the mask (out of lung space into chest wall), in which case the NCCC is computed only over the masked (lung) pixels, requiring a separate calc of Syy and kernel avg over just those points

aStatsCorrCirc(short[][][], float[][][][]) - Static method in class woSource.math.ImgProc

intentionally want non-parallel version, perhaps for small region analysis

aStatsCorrCirc(short[][][], float[][][][], boolean[][][]) - Static method in class woSource.math.ImgProc

WO version to use mask to speed up computation (which it does)

aStatsCorrCirc(short[][][], float[][][], boolean[][][]) - Static method in class woSource.math.ImgProc

aStatsCorrCirc(short[][][], float[][][]) - Static method in class woSource.math.ImgProc

aStatsCorrCirc(short[][][], float[][][][], int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

aStatsCorrCirc(short[][][], float[][][][], boolean, int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

aStatsCorrCirc(short[][][], float[][][], int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

aStatsCorrCirc(short[][][], float[][][], boolean, int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

aStatsCorrCirc(short[][][], float[][][], boolean, boolean[][][], int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

atan() - Method in class woSource.math.Complex

atan(Complex) - Static method in class woSource.math.Complex

atan(double) - Static method in class woSource.math.MathI

atan(float) - Static method in class woSource.math.MathI

atan2(double, double) - Static method in class woSource.math.MathI

atan2(float, float) - Static method in class woSource.math.MathI

atanh() - Method in class woSource.math.Complex

atanh(Complex) - Static method in class woSource.math.Complex

atanh(double) - Static method in class woSource.math.MathI

autoCropHilumVessels - Variable in class woSource.humanLungSegm

autoRun - Variable in class woSource.VesselSegm

autoRunButtonAt - Variable in class woSource.AirwaySegm

autoSaveParams - Variable in class woSource.ImageRegistration

autoSaveParams - Variable in class woSource.ImgRegistration

autoThreshold(byte[][]) - Static method in class woSource.math.ImgProc

returns the threshold value as int, and applies the threshold to the image based on ij.byteProcessor().getAutoThreshold()

autoThreshold(byte[][][]) - Static method in class woSource.math.ImgProc

autoThreshold(short[][]) - Static method in class woSource.math.ImgProc

WO 8/30/2010 for short images

autoThreshold(short[][][]) - Static method in class woSource.math.ImgProc

AutoWindowLevel - Class in woSource

AutoWindowLevel(ImagePlus) - Constructor for class woSource.AutoWindowLevel

AutoWindowLevel(ImagePlus, String) - Constructor for class woSource.AutoWindowLevel

autoWindowLevel() - Method in class woSource.math.ArrayDisplay

8/15/2012 previously this func did not actually affect the image, now it does

availDOF - Variable in class woSource.math.VesselBranch

average() - Method in class woSource.ImageOverlay

Average_Sep - Variable in class woSource.InteractiveSnake.Snake

avers() - Method in class woSource.math.Complex

avers(Complex) - Static method in class woSource.math.Complex

avg(byte[]) - Static method in class woSource.math.ArraysI

avg(byte[][]) - Static method in class woSource.math.ArraysI

avg(byte[][], int, int, int, int) - Static method in class woSource.math.ArraysI

avg(byte[][][]) - Static method in class woSource.math.ArraysI

avg(byte[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

avg(int[]) - Static method in class woSource.math.ArraysI

avg(int[][]) - Static method in class woSource.math.ArraysI

avg(int[][], int, int, int, int) - Static method in class woSource.math.ArraysI

avg(int[][][]) - Static method in class woSource.math.ArraysI

avg(int[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

avg(short[]) - Static method in class woSource.math.ArraysI

avg(short[][]) - Static method in class woSource.math.ArraysI

avg(short[][], int, int, int, int) - Static method in class woSource.math.ArraysI

avg(short[][][]) - Static method in class woSource.math.ArraysI

avg(short[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

avg(float[]) - Static method in class woSource.math.ArraysI

avg(float[][]) - Static method in class woSource.math.ArraysI

avg(float[][], int, int, int, int) - Static method in class woSource.math.ArraysI

avg(float[][][]) - Static method in class woSource.math.ArraysI

avg(float[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

avg(double[]) - Static method in class woSource.math.ArraysI

avg(double[][]) - Static method in class woSource.math.ArraysI

avg(double[][], int, int, int, int) - Static method in class woSource.math.ArraysI

avg(double[][][]) - Static method in class woSource.math.ArraysI

avg(double[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

avgEndoLambda - Variable in class woSource.math.HeartLongAxis

avgRad - Variable in class woSource.math.VesselBranch

avgToCenter() - Method in class woSource.DoseReader

avgToCenter() - Method in class woSource.DoseReader_Oct2012_oldUR

B

backTraceToMostOffendingBranch(int) - Method in class woSource.VesselSegm

backTraceToMostOffendingBranch(int, int) - Method in class woSource.VesselSegm

badAngleThresh - Variable in class woSource.VesselSegm

BartlettWindow(int, float, float) - Static method in class woSource.math.MathII

Bartlett window

batchRunHLS() - Method in class woSource.humanLungSegm

BeadFinder - Class in woSource

BeadFinder() - Constructor for class woSource.BeadFinder

beadKernel(int) - Static method in class woSource.math.MathII

WO 10/30/00 generic-sized bead gradient profile kernel

beadKernel3D(int) - Static method in class woSource.math.MathII

WO 4/23/02 spherically symmetric bead

beadProfile(int, float) - Static method in class woSource.math.MathII

WO 10/30/00 created generic-sized bead profile kernel

BGcolor - Variable in class woSource.ScreenSelectorCanvas

BGimage - Variable in class woSource.math.VesselBranch

bigEndianTransferSyntax - Variable in class woSource.DicomAnon

bigVesselBrightness - Variable in class woSource.VesselSegm

bigVesselCloseOpRadius - Variable in class woSource.humanLungSegm

binClass - Class in woSource

Adjusts the starting levels for binning histogram to minimize image info

binClass(int) - Constructor for class woSource.binClass

binClass(int[]) - Constructor for class woSource.binClass

binImage(short[][][], int[]) - Static method in class woSource.math.ImgProc

assumes bin centers based on 0..255 (or 128 or whatever) image range == histo

binImage(short[][][], int) - Static method in class woSource.math.ImgProc

biThreshold(byte[][][], int, int) - Static method in class woSource.math.ImgProc

threshold to middle range, including the min,max thresh values.

biThreshold(short[][][], int, int) - Static method in class woSource.math.ImgProc

BitMaskToArray1D(byte[][]) - Static method in class woSource.math.ArraysI

BitMaskToArray1D(byte[][][]) - Static method in class woSource.math.ArraysI

BMcoeffsToString() - Method in class woSource.ImageRegistrationPS

bodyRect - Variable in class woSource.VesselSegm

bodyROI - Variable in class woSource.humanLungSegm

bodyThresh - Variable in class woSource.AirwaySegm

bodyThresh - Variable in class woSource.humanLungSegm

bodyThresh - Variable in class woSource.PulmonaryTrunkSegm

booleanImage - Variable in class woSource.math.ArrayDisplay

Branches - Variable in class woSource.math.VesselTree

branchExists(int) - Method in class woSource.math.VesselTree

branchRadRatioThresh - Variable in class woSource.VesselSegm

brFrom - Variable in class woSource.math.HyperSkelPair

C

calc_cc() - Method in class woSource.ImageOverlay

calc_dist_map(int, float) - Method in class woSource.RegisterSnake

calcAllLIDCfirstPass() - Method in class woSource.noduleDetection

calcAllLIDCmasks() - Method in class woSource.noduleDetection

calcAvgRadius() - Method in class woSource.math.VesselBranch

calcAvgRadius(int) - Method in class woSource.math.VesselBranch

calcAvgRadius(int, int) - Method in class woSource.math.VesselBranch

calcAvgStDev() - Method in class woSource.math.SimTagImageInfo

calcCircKernel(int) - Static method in class woSource.math.MathII

WO 5/9/02 new arc integral calc versions ..

CalcCorr(float[]) - Method in class woSource.HistoMR_registration

CalcCorr(float[]) - Method in class woSource.ImageRegistration

calcDeformedMRseries(int) - Method in class woSource.ImageRegistrationPS

calcDeformedTagseries(int, int) - Method in class woSource.ImageRegistrationPS

CalcError(float[]) - Method in class woSource.math.OptMath

CalcErrorDerivs(float[], float[], int) - Method in class woSource.math.OptMath

calcFAs() - Method in class woSource.DTIanalysis

calcImageAvgSyy(byte[][][], boolean[][][]) - Static method in class woSource.ImageRegistrationPS

calcImageAvgSyy(short[][][], boolean[][][]) - Static method in class woSource.ImageRegistrationPS

calcKall(float, float, float, float, float) - Method in class woSource.LIDCreview

public NoduleCandidate NCCCtestLoc(NoduleCandidate candAt, float radAt, float padAt) { // now want to try sub-pixel shifts at this best radius byte[][][] corrAll; // will process together the 3 shifts at each krad Point3D bestFitLoc3D = new Point3D(); NoduleCandidate bestFitLoc = new NoduleCandidate(); float[][][] kshift; // check span of sub-pixel locations around this one: 5x5x5 = 125 places // these shifts are in units of pixels, unique for each direction.

calcKall(float, float, float, float, float, float, float, float) - Method in class woSource.LIDCreview

calcKall(float, float, float, float, float) - Method in class woSource.noduleDetection

calcKall(float, float, float, float, float, float, float, float) - Method in class woSource.noduleDetection

calcKall(float, float, float, float, float) - Method in class woSource.noduleDetectionModule

calcKall(float, float, float, float, float, float, float, float) - Method in class woSource.noduleDetectionModule

calcLikelyPQs(double[], boolean[][]) - Method in class woSource.LIDCtruthOpt

CalcNCCC() - Method in class woSource.ImageRegistration

CalcNCCC() - Method in class woSource.ImageRegistrationPS

CalcNMI() - Method in class woSource.ImageRegistration

calcPlaneThroughPoints(Point3Dint[]) - Static method in class woSource.math.ImgProc

8/6/2012 intent to find normal to plane passing through the given points, using plane = ax + by + cz + d =0 where the normal = {a,b,c} and the plane passes through the centroid of the poitns array (I think this is arbitrary -- can pick any point -- since I only care about the normal direction.

calcPlaneThroughPoints(int[], int[], int[]) - Static method in class woSource.math.ImgProc

calcPQs(boolean[], boolean[][]) - Method in class woSource.LIDCtruthOpt

calcRoiAndMask(int, int, int, VesselBranch) - Method in class woSource.math.VesselBranch

Intent is to create a mask the contains the region around a given branch node over which to compute the correlation (NCCC) to the original image, for optimizing the branch radius.

calcSimTagAvgStDev() - Method in class woSource.ImageRegistrationPS

currently not using until I verify that it does not change meaningfully

calcSphericalKernel(int) - Static method in class woSource.math.MathII

create spherical kernal assuming isotropic voxels of size matching gaussian kernel of same radius.

CalcStep(float[], float) - Method in class woSource.math.OptMath

calcSurfMiss(float[][]) - Method in class woSource.math.HeartLongAxis

calcTotalLikelihood(boolean[], boolean[][], double[][]) - Method in class woSource.LIDCtruthOpt

calcTruthWeights(double[], boolean[][], double[][]) - Method in class woSource.LIDCtruthOpt

cand_search_dist_max - Variable in class woSource.InteractiveSnake.Snake

Candidates(int) - Constructor for class woSource.InteractiveSnake.Candidates

Candidates(InteractiveSnake.Candidates) - Constructor for class woSource.InteractiveSnake.Candidates

candidateSep(NoduleCandidate, NoduleCandidate) - Method in class woSource.LIDCreview

NoduleCandidate[][][] candTrials; float[] testRadii = {1f, 1.1f, 1.2f, 1.3f, 1.4f, 1.5f, 1.6f, 1.7f, 1.8f, 1.9f, 2f, 2.2f, 2.4f, 2.6f, 2.8f, 3f, 3.5f, 4f, 4.5f, 5f, 5.5f, 6f, 6.5f, 7f, 7.5f, 8f, 8.5f, 9f}; float[] testPaddings = {1.5f, 2f, 2.5f, 3f}; public void gatAllPtsTrials() { candTrials = new NoduleCandidate[NtrainingNods][testRadii.length][testPaddings.length]; } public void getPtTrials(int firstPtCand, int ptAt) { String studyDirAt = new String(nodsOfInterest[firstPtCand].patientID); int l = firstPtCand; // if (origAd != null) origAd.destroy(); // System.gc(); // read in the image data for that study getPtInputDirInfo(studyDirAt); // sets LIDCstudyInputDir, LIDCnImages & LIDCimageExt.

candidateSep(Point3D, NoduleCandidate) - Method in class woSource.LIDCreview

cart2prosph(float, float, float) - Method in class woSource.math.HeartLongAxis

cart2prosph(float[]) - Method in class woSource.math.HeartLongAxis

cart2prosph(Point3D) - Method in class woSource.math.HeartLongAxis

cart2prosph(double, double, double) - Method in class woSource.math.HeartLongAxis

cart2prosph(double[]) - Method in class woSource.math.HeartLongAxis

cart2prosph(float[][]) - Method in class woSource.math.HeartLongAxis

cart2prosph(double[][]) - Method in class woSource.math.HeartLongAxis

cart2prosph(float, float, float, float) - Static method in class woSource.math.MathII

cart2prosph(float[], float) - Static method in class woSource.math.MathII

cart2prosph(double[], double) - Static method in class woSource.math.MathII

cart2prosph(double, double, double, double) - Static method in class woSource.math.MathII

cart2sph(float, float, float) - Static method in class woSource.math.MathII

cart2sph(double, double, double) - Static method in class woSource.math.MathII

ceil(float) - Static method in class woSource.math.MathI

ceil(double) - Static method in class woSource.math.MathI

CellMigration - Class in woSource

CellMigration(float[][][][], float, float, float, float[][][], boolean[][][], boolean[][][]) - Constructor for class woSource.CellMigration

CENTER - Variable in class woSource.GenericRecallableDialog

centroid() - Method in class woSource.math.Polygon2D

centroid() - Method in class woSource.math.Polygon3D

cenx - Variable in class woSource.lungSnake

ceny - Variable in class woSource.lungSnake

changeDicomInfo(byte[], String[][]) - Method in class woSource.DicomAnon

checkRemoveHyperskelPair(Point3Dint) - Method in class woSource.VesselSegm

children - Variable in class woSource.math.VesselBranch

cleanGlobalMask() - Method in class woSource.DoseVsIntensity

cleanUpMask(boolean[][][], float, float, float, int, int, int) - Static method in class woSource.math.ImgProc

WO 12/21/2014 clean up mask to remove internal holes and edge noise.

clear() - Method in class woSource.math.HeartLongAxis

Clear() - Method in class woSource.math.HyperSkelPair

clear() - Method in class woSource.math.Point2D

clear() - Method in class woSource.math.Point3D

clear() - Method in class woSource.math.Point3Dint

clear() - Method in class woSource.math.Point4D

clear() - Method in class woSource.math.Point4Dint

clear() - Method in class woSource.math.Skeletonize3D

clear() - Method in class woSource.math.VesselBranch

clear() - Method in class woSource.math.VesselTree

clearOverlays() - Method in class woSource.math.ArrayDisplay

ClearPts() - Method in class woSource.InteractiveSnake.Candidates

ClearPts() - Method in class woSource.InteractiveSnake.SmoothSnake

ClearPts() - Method in class woSource.InteractiveSnake.Snake

ClearSmoothPts() - Method in class woSource.InteractiveSnake.Snake

clip(byte[][], int) - Static method in class woSource.math.ImgProc

cut off above thresh

clip(byte[][][], int) - Static method in class woSource.math.ImgProc

clip(byte[][], int, int) - Static method in class woSource.math.ImgProc

clip(byte[][][], int, int) - Static method in class woSource.math.ImgProc

clip(short[][], int) - Static method in class woSource.math.ImgProc

clip(short[][][], int) - Static method in class woSource.math.ImgProc

clip(short[][], int, int) - Static method in class woSource.math.ImgProc

clip(short[][][], int, int) - Static method in class woSource.math.ImgProc

clip(int[][], int) - Static method in class woSource.math.ImgProc

clip(int[][][], int) - Static method in class woSource.math.ImgProc

clip(int[][], int, int) - Static method in class woSource.math.ImgProc

clip(int[][][], int, int) - Static method in class woSource.math.ImgProc

clip(float[][], float) - Static method in class woSource.math.ImgProc

clip(float[][][], float) - Static method in class woSource.math.ImgProc

clip(float[][], float, float) - Static method in class woSource.math.ImgProc

clip(float[][][], float, float) - Static method in class woSource.math.ImgProc

clipbelow(short[][], int) - Static method in class woSource.math.ImgProc

cut off below thresh.

clipbelow(short[][][], int) - Static method in class woSource.math.ImgProc

clipbelow(short[][], int, int) - Static method in class woSource.math.ImgProc

clipbelow(short[][][], int, int) - Static method in class woSource.math.ImgProc

clipbelow(int[][], int) - Static method in class woSource.math.ImgProc

clipbelow(int[][][], int) - Static method in class woSource.math.ImgProc

clipbelow(int[][], int, int) - Static method in class woSource.math.ImgProc

clipbelow(int[][][], int, int) - Static method in class woSource.math.ImgProc

clipbelow(float[][], float) - Static method in class woSource.math.ImgProc

clipbelow(float[][][], float) - Static method in class woSource.math.ImgProc

clipbelow(float[][], float, float) - Static method in class woSource.math.ImgProc

clipbelow(float[][][], float, float) - Static method in class woSource.math.ImgProc

clipBigPtSeps(InteractiveSnake.Snake, int, int) - Method in class woSource.lungSnake

clipBigPtSeps(InteractiveSnake.Snake, int, int) - Method in class woSource.noduleDetection.lungSnake

clipBranchRadiusIncreases(int, float, float) - Method in class woSource.math.VesselTree

returns first break point along this branch
Intended to find fibrotic regions in lung volume hit during vessel traversal

clipRadiusIncreases(float, float) - Method in class woSource.math.VesselTree

Found that parRadRatioThresh of 1.5 and radIncrRatio of 2 worked OK for 2D test data.

clone() - Method in class woSource.math.Complex

close() - Method in class woSource.InteractiveSnake_Hermite

close() - Method in class woSource.InteractiveSnake_Hermite3D

closeOp(boolean[][][], float, float, boolean[][][]) - Static method in class woSource.math.ImgProc

closeOp(byte[][], int) - Static method in class woSource.math.ImgProc

binary image operation Close = erode(dilate(A))

closeOp(byte[][], int, Rectangle) - Static method in class woSource.math.ImgProc

closeOp(byte[][][], int) - Static method in class woSource.math.ImgProc

closeOp(byte[][][], int, Rectangle3D) - Static method in class woSource.math.ImgProc

closeOp(byte[][][], int, float) - Static method in class woSource.math.ImgProc

closeOp(byte[][][], int, float, Rectangle3D) - Static method in class woSource.math.ImgProc

closeOp(byte[][], float) - Static method in class woSource.math.ImgProc

closeOp(byte[][], float, Rectangle) - Static method in class woSource.math.ImgProc

closeOp(byte[][][], float) - Static method in class woSource.math.ImgProc

closeOp(byte[][][], float, Rectangle3D) - Static method in class woSource.math.ImgProc

closeOp(byte[][][], float, float) - Static method in class woSource.math.ImgProc

closeOp(byte[][][], float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

closeOp(boolean[][], int) - Static method in class woSource.math.ImgProc

closeOp(boolean[][], int, Rectangle) - Static method in class woSource.math.ImgProc

closeOp(boolean[][][], int) - Static method in class woSource.math.ImgProc

closeOp(boolean[][][], int, Rectangle3D) - Static method in class woSource.math.ImgProc

closeOp(boolean[][][], int, float) - Static method in class woSource.math.ImgProc

closeOp(boolean[][][], int, float, Rectangle3D) - Static method in class woSource.math.ImgProc

closeOp(boolean[][], float) - Static method in class woSource.math.ImgProc

closeOp(boolean[][], float, Rectangle) - Static method in class woSource.math.ImgProc

closeOp(boolean[][][], float) - Static method in class woSource.math.ImgProc

closeOp(boolean[][][], float, Rectangle3D) - Static method in class woSource.math.ImgProc

closeOp(boolean[][][], float, float) - Static method in class woSource.math.ImgProc

closeOp(boolean[][][], float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

closingOpSize - Variable in class woSource.VesselSegm

ColonSegm - Class in woSource

ColonSegm() - Constructor for class woSource.ColonSegm

colorsList - Static variable in class woSource.math.MathI

combinedRoi(Rectangle3D) - Method in class woSource.math.Rectangle3D

Complex - Class in woSource.math

Complex() - Constructor for class woSource.math.Complex

Complex(double, double) - Constructor for class woSource.math.Complex

Complex(double) - Constructor for class woSource.math.Complex

Complex(Complex) - Constructor for class woSource.math.Complex

Compliment(boolean[][], boolean[][]) - Static method in class woSource.math.ArraysI

boolean compliment operator = the part of A that is not also a part of B (almost == A - B)

Compliment(boolean[][][], boolean[][][]) - Static method in class woSource.math.ArraysI

boolean compliment operator = the part of A that is not also a part of B (almost == A - B)

Compliment(byte[][], byte[][]) - Static method in class woSource.math.ArraysI

Compliment(byte[][][], byte[][][]) - Static method in class woSource.math.ArraysI

computeAreaUnderArc(float, float, float) - Static method in class woSource.math.MathII

computeCircularContour() - Method in class woSource.DVHCalc

computeCylPartialVol(float, float, float, float, float, float, float[], float, float, float, float, float) - Static method in class woSource.math.MathII

WO 03/18/2013 using the approach above to merely break up the test voxel (3D) into little voxels to compute the partial volume for a cylinder passing near the voxel.

computeCylPartialVol(float, float, float, float, float[], float, float, float, float) - Static method in class woSource.math.MathII

WO 03/18/2013 2D version of the above.

computeDoseResponse(int) - Method in class woSource.DoseVsIntensity

ComputeDoseSpread() - Method in class woSource.DoseCalc

computeDoseVolumes(int) - Method in class woSource.DoseVolumeStats

computeDTs() - Method in class woSource.DTIanalysis

computeDVH() - Method in class woSource.DVHCalc

computeEdgeImage(byte[][][]) - Method in class woSource.HeartSegm

computeEdgeImage(byte[][]) - Method in class woSource.HeartSegm

computeEdgeImage(short[][][]) - Method in class woSource.HeartSegm

computeEdgeImage(short[][]) - Method in class woSource.HeartSegm

computeEdgeImage(byte[][][]) - Method in class woSource.InteractiveSnake

computeEdgeImage(short[][][]) - Method in class woSource.InteractiveSnake

computeGrad3D() - Method in class woSource.GradientAnalysis3D

computeImage() - Method in class woSource.math.SimTagImageInfo

computeNodes() - Method in class woSource.math.VesselBranch

fit a smooth curve through the centerline points

computeOnePixel3dArcVol(float, float, float, float, float, float, float) - Static method in class woSource.math.MathII

WO 1/31/11 this seems to give wrong answers sometimes.

computePixel3dArcVol(float, float, float, float, float, float, float) - Static method in class woSource.math.MathII

WO 01/31/11 tetrahedron calc seems to fail for some arrangements of the pixel alignment trying simply breaking the cube up into many cubes and doing cube-sum.

computePixelArcArea(float, float, float, float, float) - Static method in class woSource.math.MathII

computePSF() - Method in class woSource.Deconvolver

computeRoiStats(String, short[][][], Roi) - Method in class woSource.MouseMicroCTlungSegm

computeSeriesPtTangent(float[][], int) - Method in class woSource.math.VesselBranch

WO 9/3/2015 compute tangent to the the array of points passed in, in mm Intended for tangent for smoothPts, but generalized also for fitted bifurcation pts.

computeSmoothPts(float[]) - Method in class woSource.math.VesselBranch

Fit a smooth curve through the centerline points.

computeSmoothPtsLen() - Method in class woSource.math.VesselBranch

computeSmoothPtTangent(int) - Method in class woSource.math.VesselBranch

compute tangent to the smoothPts, in mm

computeSpherePartialVol(float, float, float, float, float, float, float, float, float, float) - Static method in class woSource.math.MathII

WO 08/11/2015 using the approach above to merely break up the test voxel (3D) into little voxels to compute the partial volume for a cylinder passing near the voxel.

computeSpherePartialVol(float, float, float, float, float, float, float) - Static method in class woSource.math.MathII

WO 8/11/2015 2D version of the above.

computeSphericalContour() - Method in class woSource.DVHCalc

computeStats(short[][][], boolean[][][]) - Method in class woSource.MouseLungSegmentor

computeStats(short[][][], boolean[][][]) - Method in class woSource.MouseMicroCTlungSegm

computeStats(short[][], boolean[][]) - Method in class woSource.MouseMicroCTlungSegm

computeThinImage() - Method in class woSource.math.Skeletonize3D

computeVoxelEndoLambdas(ContourFit) - Method in class woSource.ImageRegistrationPS

con_ptSep - Variable in class woSource.HeartSegm

confit - Variable in class woSource.HeartSegm

conjugate(Complex) - Static method in class woSource.math.Complex

conjugate() - Method in class woSource.math.Complex

connectEndsForMask - Variable in class woSource.lungSnake

connTissueMask - Variable in class woSource.VesselSegm

conSnakeStacks - Variable in class woSource.HeartSegm

contains(int, int) - Method in class woSource.math.Polygon2D

contains(double, double) - Method in class woSource.math.Polygon2D

contains(float, float) - Method in class woSource.math.Polygon2D

4/23/11 when checking right or up still had problems when > saddle point,
so adding check left and up.

contains(Polygon2D) - Method in class woSource.math.Polygon2D

contains(int, int) - Method in class woSource.math.Polygon3D

contains(double, double) - Method in class woSource.math.Polygon3D

contains(float, float, float) - Method in class woSource.math.Rectangle3D

contains_down(float, float) - Method in class woSource.math.Polygon2D

Return true if thinks the given point is inside the polygon checking down.

contains_downUp(float, float, boolean) - Method in class woSource.math.Polygon2D

Return true if thinks the given point is inside the polygon checking down.

contains_left(float, float) - Method in class woSource.math.Polygon2D

contains_right(float, float) - Method in class woSource.math.Polygon2D

Return true if thinks the given point is inside the polygon checking right.

contains_rightLeft(float, float, boolean) - Method in class woSource.math.Polygon2D

Return true if thinks the given point is inside the polygon when checking right.

contains_up(float, float) - Method in class woSource.math.Polygon2D

ContourFit - Class in woSource

ContourFit(float[][][][], int[][], HeartLongAxis[], int, int) - Constructor for class woSource.ContourFit

contourPts - Variable in class woSource.ContourFit

contourPts - Variable in class woSource.HeartSegm

Contours - Variable in class woSource.SnakeReader

contoursOnly - Variable in class woSource.HeartSegm

contrastWasUsed - Variable in class woSource.math.VesselBranch

convDose2CTscannerCoords(Properties[], Point3D, Rectangle3D, float[], float[], float[]) - Method in class woSource.DoseReader

returns the shifts needed to align the dose field to the image set, and // sets doseDepths, widths, heights [mm] and other parameters read from dicom header // WO 10/12/2012 modified to use dose data as 3D dicom image.

convertConSnakePtsToArray() - Method in class woSource.HeartSegm

ConvertToDicom - Class in woSource

intent is to use the dicom header info from a donor image or stack to save a non-dicom data set as dicom with those attributes

ConvertToDicom() - Constructor for class woSource.ConvertToDicom

ConvertToDicom(ImagePlus, short[][][], String, String) - Constructor for class woSource.ConvertToDicom

ConvertToDicom(ImagePlus, short[][][], String, String, boolean) - Constructor for class woSource.ConvertToDicom

ConvertToDicom(ImagePlus, short[][][], String, String, String, boolean) - Constructor for class woSource.ConvertToDicom

ConvertToDicom(ImagePlus, byte[][][], String, String) - Constructor for class woSource.ConvertToDicom

ConvertToDicom(ImagePlus, byte[][][], String, String, boolean) - Constructor for class woSource.ConvertToDicom

ConvertToDicom(ImagePlus, byte[][][], String, String, String, boolean) - Constructor for class woSource.ConvertToDicom

convolve(float[][], float[][]) - Static method in class woSource.math.ImgProc

2D convolution.

convolve(byte[][], float[][]) - Static method in class woSource.math.ImgProc

convolve(int[][], float[][]) - Static method in class woSource.math.ImgProc

convolve(short[][], float[][]) - Static method in class woSource.math.ImgProc

convolve(byte[][][], float[][][], int, int) - Static method in class woSource.math.ImgProc

3D convolution
ArrayDisplay & NR conventions are pixels[depth][width][height]
these functions directly below are meant to be invoked by the //-computing functions below them.

convolve(byte[][][], float[][][], int, int, int) - Static method in class woSource.math.ImgProc

WO 5/24/2012 skipval probably going to be 0 -- don't bother computing for points outside the image.

convolve(short[][][], float[][][], int, int) - Static method in class woSource.math.ImgProc

convolve(int[][][], float[][][], int, int) - Static method in class woSource.math.ImgProc

convolve(float[][][], float[][][], int, int) - Static method in class woSource.math.ImgProc

convolve(byte[][][], float[][][], int) - Static method in class woSource.math.ImgProc

WO 5/25/2012 modified to run in //, split slices up.

convolve(byte[][][], float[][][]) - Static method in class woSource.math.ImgProc

convolve(short[][][], float[][][]) - Static method in class woSource.math.ImgProc

convolve(int[][][], float[][][]) - Static method in class woSource.math.ImgProc

convolve(float[][][], float[][][]) - Static method in class woSource.math.ImgProc

convolveFreq(float[][][], float[][]) - Static method in class woSource.math.ImgProc

convolution usign fourier tranforms.

convolveFreq(short[][][], float[][]) - Static method in class woSource.math.ImgProc

convolveFreq(short[][][], float[][][]) - Static method in class woSource.math.ImgProc

convolveFreq(byte[][][], float[][][]) - Static method in class woSource.math.ImgProc

convolveFreq(int[][][], float[][][]) - Static method in class woSource.math.ImgProc

convolveFreq(float[][][], float[][][]) - Static method in class woSource.math.ImgProc

ConvolveThread(byte[][][], float[][][], int, int, int) - Constructor for class woSource.math.ImgProc.ConvolveThread

ConvolveThread(byte[][][], float[][][], int, int) - Constructor for class woSource.math.ImgProc.ConvolveThread

ConvolveThread(short[][][], float[][][], int, int) - Constructor for class woSource.math.ImgProc.ConvolveThread

ConvolveThread(int[][][], float[][][], int, int) - Constructor for class woSource.math.ImgProc.ConvolveThread

ConvolveThread(float[][][], float[][][], int, int) - Constructor for class woSource.math.ImgProc.ConvolveThread

ConZs - Variable in class woSource.SnakeReader

Coords - Variable in class woSource.FEnodeClass

Copy(ImageRegistration) - Method in class woSource.ImageRegistration

Copy(ImageRegistrationPS) - Method in class woSource.ImageRegistrationPS

Copy(InteractiveSnake.Candidates) - Method in class woSource.InteractiveSnake.Candidates

Copy(InteractiveSnake.SmoothSnake) - Method in class woSource.InteractiveSnake.SmoothSnake

Copy(InteractiveSnake.Snake) - Method in class woSource.InteractiveSnake.Snake

Copy(InteractiveSnake.SnakeStack) - Method in class woSource.InteractiveSnake.SnakeStack

copy(boolean[][], boolean[][]) - Static method in class woSource.math.ArraysI

copy(boolean[][]) - Static method in class woSource.math.ArraysI

copy(boolean[][][], boolean[][][]) - Static method in class woSource.math.ArraysI

copy(boolean[][][]) - Static method in class woSource.math.ArraysI

copy(boolean[][][][], boolean[][][][]) - Static method in class woSource.math.ArraysI

copy(boolean[][][][]) - Static method in class woSource.math.ArraysI

copy(byte[][], byte[][]) - Static method in class woSource.math.ArraysI

copy(byte[][]) - Static method in class woSource.math.ArraysI

copy(byte[][][], byte[][][]) - Static method in class woSource.math.ArraysI

copy(byte[][][]) - Static method in class woSource.math.ArraysI

copy(byte[][][][], byte[][][][]) - Static method in class woSource.math.ArraysI

copy(byte[][][][]) - Static method in class woSource.math.ArraysI

copy(short[][], short[][]) - Static method in class woSource.math.ArraysI

copy(short[][]) - Static method in class woSource.math.ArraysI

copy(short[][][], short[][][]) - Static method in class woSource.math.ArraysI

copy(short[][][][], short[][][][]) - Static method in class woSource.math.ArraysI

copy(short[][][]) - Static method in class woSource.math.ArraysI

copy(short[][][][]) - Static method in class woSource.math.ArraysI

copy(int[], int[]) - Static method in class woSource.math.ArraysI

copy(int[]) - Static method in class woSource.math.ArraysI

copy(int[][], int[][]) - Static method in class woSource.math.ArraysI

copy(int[][]) - Static method in class woSource.math.ArraysI

copy(int[][][], int[][][]) - Static method in class woSource.math.ArraysI

copy(int[][][]) - Static method in class woSource.math.ArraysI

copy(float[], float[]) - Static method in class woSource.math.ArraysI

copy(float[]) - Static method in class woSource.math.ArraysI

copy(float[][], float[][]) - Static method in class woSource.math.ArraysI

copy(float[][]) - Static method in class woSource.math.ArraysI

copy(float[][][], float[][][]) - Static method in class woSource.math.ArraysI

copy(float[][][]) - Static method in class woSource.math.ArraysI

copy(float[][][][]) - Static method in class woSource.math.ArraysI

copy(double[]) - Static method in class woSource.math.ArraysI

copy(double[][], double[][]) - Static method in class woSource.math.ArraysI

copy(double[][]) - Static method in class woSource.math.ArraysI

copy(Complex) - Static method in class woSource.math.Complex

copy() - Method in class woSource.math.Complex

copy(Complex[]) - Static method in class woSource.math.Complex

copy(Complex[][]) - Static method in class woSource.math.Complex

copy(Complex[][][]) - Static method in class woSource.math.Complex

Copy(HeartLongAxis) - Method in class woSource.math.HeartLongAxis

Copy(HyperSkelPair) - Method in class woSource.math.HyperSkelPair

Copy(Image3Dinfo) - Method in class woSource.math.Image3Dinfo

Copy(LIDCnodule) - Method in class woSource.math.LIDCnodule

Copy(NoduleCandidate) - Method in class woSource.math.NoduleCandidate

Copy(Point2D) - Method in class woSource.math.Point2D

Copy(Point3D) - Method in class woSource.math.Point3D

Copy(Point3Dint) - Method in class woSource.math.Point3Dint

Copy(Point3D) - Method in class woSource.math.Point4D

Copy(Point4D) - Method in class woSource.math.Point4D

Copy(Point3Dint) - Method in class woSource.math.Point4Dint

Copy(Point4Dint) - Method in class woSource.math.Point4Dint

Copy(Rectangle3D) - Method in class woSource.math.Rectangle3D

Copy(SimTagImageInfo) - Method in class woSource.math.SimTagImageInfo

Copy(VesselTree) - Method in class woSource.math.VesselTree

CopyAll(VesselBranch) - Method in class woSource.math.VesselBranch

copyOutsideRoi(boolean[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

copyOutsideRoi(byte[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

CopyPts(InteractiveSnake.Snake) - Method in class woSource.InteractiveSnake.Snake

CopyPts(VesselBranch) - Method in class woSource.math.VesselBranch

corrAd - Variable in class woSource.noduleDetectionModule

CorrCalcThread(short[][][], float[][][][], boolean[][][], int, int, int, int, int, int) - Constructor for class woSource.math.ImgProc.CorrCalcThread

correlation(float[][], float[][]) - Static method in class woSource.math.ImgProc

2D correlation.

correlation(short[][], float[][]) - Static method in class woSource.math.ImgProc

correlation(float[][][], float[][]) - Static method in class woSource.math.ImgProc

correlation(short[][][], float[][]) - Static method in class woSource.math.ImgProc

correlation(float[][][], float[][][]) - Static method in class woSource.math.ImgProc

correlation(short[][][], float[][][]) - Static method in class woSource.math.ImgProc

corrValue - Variable in class woSource.math.NoduleCandidate

cos() - Method in class woSource.math.Complex

cos(Complex) - Static method in class woSource.math.Complex

cos(double) - Static method in class woSource.math.MathI

cos(float) - Static method in class woSource.math.MathI

cosh() - Method in class woSource.math.Complex

cosh(Complex) - Static method in class woSource.math.Complex

cosh(double) - Static method in class woSource.math.MathI

cosh(float) - Static method in class woSource.math.MathI

cot() - Method in class woSource.math.Complex

cot(Complex) - Static method in class woSource.math.Complex

coth() - Method in class woSource.math.Complex

coth(Complex) - Static method in class woSource.math.Complex

coth(double) - Static method in class woSource.math.MathI

covers() - Method in class woSource.math.Complex

covers(Complex) - Static method in class woSource.math.Complex

create3BrTestTree() - Method in class woSource.VesselSegm

create3DcrossingTestTree() - Method in class woSource.VesselSegm

create3DTemplate - Class in woSource

create3DTemplate() - Constructor for class woSource.create3DTemplate

createBifurcationMesh(VesselBranch) - Method in class woSource.math.VesselBranch

goal to create the surface mesh that interpolates from the parent to this child.

createCrossingCylSimImage() - Method in class woSource.VesselSegm

createCylinderTestSimImage() - Method in class woSource.VesselSegm

createDicomProps(ImagePlus) - Static method in class woSource.math.ImgProc

createDicomProps(ImagePlus, String) - Static method in class woSource.math.ImgProc

createDicomProps(ImagePlus, float, float, float) - Static method in class woSource.math.ImgProc

createDicomProps(ImagePlus, float, float, float, float, float, float, float, float, float) - Static method in class woSource.math.ImgProc

createDicomProps(ImagePlus, String, float, float, float, float, float, float, float, float, float) - Static method in class woSource.math.ImgProc

props field is blank -- probably not a dicom image, but need workable header spatial info for subsequent processing

createElemSimImage(byte[][][], int, Rectangle3D, VesselBranch) - Method in class woSource.math.VesselBranch

WO 3/18/2013 intent is to create an image from the current vessel info for use later as a template to match for the vessel tree.

createElemSimImage(byte[][][], int, Rectangle3D, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createElemSimImage(byte[][][], int, float, Rectangle3D, VesselBranch) - Method in class woSource.math.VesselBranch

createElemSimImage(byte[][][], int, float, float, Rectangle3D, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createHyperSkelPair(int, int, boolean, int, int, boolean) - Method in class woSource.VesselSegm

createHyperSkelPair(int, int, Point3Dint, Point3Dint) - Method in class woSource.VesselSegm

createIsotropicSimImage(byte[][][], VesselBranch) - Method in class woSource.math.VesselBranch

goal is to create a sim image that can be used to generate a 3D physical model via a 3D printer of the vessel tree.

createIsotropicSimImage(byte[][][], float, VesselBranch) - Method in class woSource.math.VesselBranch

createIsotropicSimImage(byte[][][], float, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createIsotropicSimImage(int, int, int) - Method in class woSource.math.VesselTree

createIsotropicSimImage(int, int, int, float) - Method in class woSource.math.VesselTree

CreateMask() - Method in class woSource.InteractiveSnake

CreateMask() - Method in class woSource.InteractiveSnake_Hermite

CreateMask() - Method in class woSource.InteractiveSnake_Hermite3D

createSimImage(int, int, int, VesselBranch) - Method in class woSource.math.VesselBranch

intent is to use the branch smoothed centerline and passed in radius to create a simulated image, based on the known voxel dimensions.

createSimImage(int, int, int, float, float, VesselBranch) - Method in class woSource.math.VesselBranch

createSimImage(Rectangle3D, VesselBranch) - Method in class woSource.math.VesselBranch

createSimImage(float, float, Rectangle3D, VesselBranch) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], VesselBranch) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], Rectangle3D, VesselBranch) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], int, int, VesselBranch) - Method in class woSource.math.VesselBranch

This relies on the smoothPts and the avgRadius to create a simulated image, up to and including smPtEnd

createSimImage(byte[][][], float, float, VesselBranch) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], float, float, Rectangle3D, VesselBranch) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], int, int, float, float, VesselBranch) - Method in class woSource.math.VesselBranch

createSimImage(int, int, int, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(int, int, int, float, float, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(Rectangle3D, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(float, float, Rectangle3D, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], Rectangle3D, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], int, int, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

This relies on the smoothPts and the avgRadius to create a simulated image, up to and including smPtEnd

createSimImage(byte[][][], float, float, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], float, float, Rectangle3D, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], float, Rectangle3D, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], float, Rectangle3D, VesselBranch, boolean, boolean) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], int, int, float, float, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], int, int, float, float, Rectangle3D, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

createSimImage(byte[][][], boolean, int, int, float, float, Rectangle3D, VesselBranch, boolean, boolean) - Method in class woSource.math.VesselBranch

intent is to use the branch smoothed centerline (in pixel units) and passed in radius (in mm) to create a simulated image, based on the known voxel dimensions.

createSimImage(int, int, int) - Method in class woSource.math.VesselTree

createSimImage(int, int, int, float) - Method in class woSource.math.VesselTree

createSimImage(int, int, int, float, boolean) - Method in class woSource.math.VesselTree

createSimImage(int, int, int, Rectangle3D) - Method in class woSource.math.VesselTree

createSimImage(int, int, int, float, Rectangle3D) - Method in class woSource.math.VesselTree

createSimImage(int, int, int, float, Rectangle3D, boolean) - Method in class woSource.math.VesselTree

createSphericalDoseProfile() - Method in class woSource.DoseCalc

createSTL() - Method in class woSource.math.VesselBranch

goal is to create an stl file to be used for CAD and 3D printing of the vessel tree.

createSTL(VesselBranch) - Method in class woSource.math.VesselBranch

createSTL() - Method in class woSource.math.VesselTree

goal is to create an stl file to be used for CAD and 3D printing of the vessel tree.

createSurfMesh() - Method in class woSource.math.VesselBranch

goal is to create an surface mesh of the fitted tubular structure to help with stl file and simulated CT.

createSurfMesh(VesselBranch) - Method in class woSource.math.VesselBranch

createTemplates(float, float, float, float, float) - Method in class woSource.noduleDetectionModule

cropDoseField(int, int, int, int, int, int) - Method in class woSource.DoseReader

cropDoseField(int, int, int, int, int, int) - Method in class woSource.DoseReader_Oct2012_oldUR

cropToObjectROI() - Method in class woSource.ImageReviewer

crop the images to objectROI.

cropToRect(Rectangle3D) - Method in class woSource.ColonSegm

cropToRect(Rectangle3D) - Method in class woSource.noduleDetectionModule

cropToRect(Rectangle3D) - Method in class woSource.PulmonaryTrunkSegm

cropToRect(Rectangle3D) - Method in class woSource.RatImageAdjuster

cropToRect(Rectangle3D) - Method in class woSource.VesselSegm

crossingHyperPair - Variable in class woSource.math.HyperSkelPair

csc() - Method in class woSource.math.Complex

csc(Complex) - Static method in class woSource.math.Complex

csch() - Method in class woSource.math.Complex

csch(Complex) - Static method in class woSource.math.Complex

csch(double) - Static method in class woSource.math.MathI

cube(double) - Static method in class woSource.math.MathI

cube(float) - Static method in class woSource.math.MathI

cube(int) - Static method in class woSource.math.MathI

cubic_rt(float, float, float) - Static method in class woSource.math.MathI

function to calc the three solutions to the cubic equation: x*x*x + a1*x*x + a2*x + a3 = 0 since two solutions may be imaginary, set up a dmatrix {3x2} (each solution, real and imag parts) to hold the solution values returns only the largest real root

cubic_rt(double, double, double) - Static method in class woSource.math.MathI

cubrt(double) - Static method in class woSource.math.MathI

lame java math lib doesn't have cube root

cubrt(float) - Static method in class woSource.math.MathI

cur_level - Variable in class woSource.WindowLevelAdjuster

cur_ptSep - Variable in class woSource.InteractiveSnake

cur_ptSep - Variable in class woSource.InteractiveSnake.Snake

cur_ptShift - Variable in class woSource.InteractiveSnake

cur_snake - Variable in class woSource.InteractiveSnake.SnakeStack

cur_window - Variable in class woSource.WindowLevelAdjuster

curEndoEpi - Variable in class woSource.HeartSegm

curEnergy_Bend - Variable in class woSource.InteractiveSnake

curEnergy_Pressure - Variable in class woSource.InteractiveSnake

curEnergy_Stretch - Variable in class woSource.InteractiveSnake

curMyoIntensity - Variable in class woSource.HeartSegm

curSeries - Variable in class woSource.HeartSegm

curSlice - Variable in class woSource.HeartSegm

cursn - Variable in class woSource.lungSnake

cursnpts - Variable in class woSource.lungSnake

curTime - Variable in class woSource.HeartSegm

customButFunc() - Method in class woSource.AirwaySegm

customButFunc() - Method in class woSource.ColonSegm

customButFunc() - Method in class woSource.humanLungSegm

customButFunc() - Method in class woSource.ImageReviewer

customButFunc() - Method in class woSource.LIDCreview

customButFunc() - Method in class woSource.noduleDetectionModule

customButFunc() - Method in class woSource.PulmonaryTrunkSegm

customButFunc() - Method in class woSource.RatImageAdjuster

customButFunc() - Method in class woSource.seededRegionGrowing

customButFunc() - Method in class woSource.VesselSegm

customButFunction() - Method in class woSource.noduleDetection

customChoiceFunc() - Method in class woSource.ImageReviewer

customChoiceFunc() - Method in class woSource.LIDCreview

D

D - Static variable in class woSource.ImageRegistration

debug - Variable in class woSource.InteractiveSnake.Snake

debug - Variable in class woSource.lungSnake

debugLungSegmen - Variable in class woSource.humanLungSegm

debugSnakes - Variable in class woSource.humanLungSegm

decimalString(double) - Static method in class woSource.math.MathII

decimalString(double, int) - Static method in class woSource.math.MathII

decimalString(float) - Static method in class woSource.math.MathII

decimalString(float, int) - Static method in class woSource.math.MathII

Deconvolver - Class in woSource

Deconvolver() - Constructor for class woSource.Deconvolver

defaultLevel - Variable in class woSource.WindowLevelAdjuster

defaultWindow - Variable in class woSource.WindowLevelAdjuster

defImgs - Variable in class woSource.math.SeriesImagesClass

defVoxelLocs - Variable in class woSource.math.SeriesImagesClass

deleteAllChildrenFromList() - Method in class woSource.math.VesselBranch

deleteBranch_MergeSiblingToParent(int) - Method in class woSource.math.VesselTree

returns true if merged.

deleteBranchAndChildren(int) - Method in class woSource.math.VesselTree

This deletes the branch with Branches array index 'indexAt' and its decendants recursively.

deleteChildFromList(int) - Method in class woSource.math.VesselBranch

deleteFirstPt() - Method in class woSource.math.VesselBranch

deleteLastPt() - Method in class woSource.math.VesselBranch

DeleteLoopLoc(int) - Method in class woSource.VesselSegm

llAt is index to current loopLoc array

deleteOrphanedBranchPt(int) - Method in class woSource.VesselSegm

deleteTopOrphanedBranchPt() - Method in class woSource.VesselSegm

deleteTree(int) - Method in class woSource.VesselSegm

DenCC() - Method in class woSource.ImageOverlay

Depth - Variable in class woSource.DoseReader

Depth - Variable in class woSource.DoseReader_Oct2012_oldUR

DEPTH - Static variable in class woSource.math.ArrayDisplay

Depth - Variable in class woSource.math.ArrayDisplay

depth - Variable in class woSource.math.Rectangle3D

depth - Variable in class woSource.math.SeriesImagesClass

Derivs - Variable in class woSource.FEmeshClass

Derivs - Variable in class woSource.FEnodeClass

DerivStepScale - Variable in class woSource.math.OptMath

destroy() - Method in class woSource.ImageRegistrationPS

destroy() - Method in class woSource.ImgRegistration

destroy() - Method in class woSource.InteractiveSnake.Candidates

destroy() - Method in class woSource.InteractiveSnake.Snake

destroy() - Method in class woSource.InteractiveSnake.SnakeStack

destroy() - Method in class woSource.math.ArrayColorDisplay3D

destroy() - Method in class woSource.math.ArrayDisplay

remove the window and clear arrays

destroy() - Method in class woSource.MIPSviewer

destroy() - Method in class woSource.MIPSviewerColor

destroy() - Method in class woSource.Point3Dviewer

destroyViewer() - Method in class woSource.math.HeartLongAxis

diameter - Variable in class woSource.math.LIDCnodule

DicomAnon - Class in woSource

DicomAnon() - Constructor for class woSource.DicomAnon

DicomAnon(String, String) - Constructor for class woSource.DicomAnon

DicomAnon(String, String, boolean) - Constructor for class woSource.DicomAnon

didAllCons - Variable in class woSource.HeartSegm

didAllCurSeriesCons() - Method in class woSource.HeartSegm

didAllSeriesCons(int) - Method in class woSource.HeartSegm

didBodyCrop - Variable in class woSource.VesselSegm

didLungCrop - Variable in class woSource.PulmonaryTrunkSegm

didVesselCrop - Variable in class woSource.VesselSegm

dilate(byte[][], int) - Static method in class woSource.math.ImgProc

WO dilate: if any pixels are ON within the circle, then turn the center ON.

dilate(byte[][], int, Rectangle) - Static method in class woSource.math.ImgProc

dilate(byte[][], float) - Static method in class woSource.math.ImgProc

dilate(byte[][], float, Rectangle) - Static method in class woSource.math.ImgProc

dilate(boolean[][], int) - Static method in class woSource.math.ImgProc

dilate(boolean[][], int, Rectangle) - Static method in class woSource.math.ImgProc

dilate(boolean[][], float) - Static method in class woSource.math.ImgProc

dilate(boolean[][], float, Rectangle) - Static method in class woSource.math.ImgProc

dilate(byte[][][], int) - Static method in class woSource.math.ImgProc

dilate(byte[][][], float) - Static method in class woSource.math.ImgProc

dilate(byte[][][], int, Rectangle3D) - Static method in class woSource.math.ImgProc

dilate(byte[][][], float, Rectangle3D) - Static method in class woSource.math.ImgProc

dilate(byte[][][], int, float) - Static method in class woSource.math.ImgProc

dilate(byte[][][], float, float) - Static method in class woSource.math.ImgProc

dilate(byte[][][], int, float, Rectangle3D) - Static method in class woSource.math.ImgProc

dilate(byte[][][], float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

dilate(boolean[][][], int) - Static method in class woSource.math.ImgProc

dilate(boolean[][][], float) - Static method in class woSource.math.ImgProc

dilate(boolean[][][], int, Rectangle3D) - Static method in class woSource.math.ImgProc

dilate(boolean[][][], float, Rectangle3D) - Static method in class woSource.math.ImgProc

dilate(boolean[][][], int, float) - Static method in class woSource.math.ImgProc

dilate(boolean[][][], float, float) - Static method in class woSource.math.ImgProc

dilate(boolean[][][], int, float, Rectangle3D) - Static method in class woSource.math.ImgProc

dilate(boolean[][][], float, float, boolean[][][]) - Static method in class woSource.math.ImgProc

WO 7/3/2012 trying version where you pass in all the points at the edge that matter for dilating.

dilate(boolean[][][], float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

WO 10/3/2012 parallel version.

dilateGray(byte[][], boolean[][]) - Static method in class woSource.math.ImgProc

11/17/2014 intent is to implement a gray-scale filling operation that assigns to each pixel the maximum of its neighbors, as indicated by the mask (kernel) image.

dilateGray(byte[][][], boolean[][]) - Static method in class woSource.math.ImgProc

dilateGray(short[][], boolean[][]) - Static method in class woSource.math.ImgProc

dilateGray(short[][][], boolean[][]) - Static method in class woSource.math.ImgProc

DilateThread(boolean[][][], float, float, Rectangle3D) - Constructor for class woSource.math.ImgProc.DilateThread

directory - Variable in class woSource.DicomAnon

disableButton(int) - Method in class woSource.GenericRecallableDialog

disableTraversal - Variable in class woSource.AirwaySegm

disconnectedSnakeEnds - Variable in class woSource.InteractiveSnake.SmoothSnake

diskTemplate(float) - Static method in class woSource.math.MathII

diskTemplate(float, float) - Static method in class woSource.math.MathII

diskTemplate(float, float, float, float) - Static method in class woSource.math.MathII

diskTemplate(float, float, float, float, float, float) - Static method in class woSource.math.MathII

WO 4/30/2013 for radius[mm] disk kernel (2D version of sphere).

displayContour() - Method in class woSource.DoseCalc

dist3DfromPt(boolean[][][], int, int, int) - Static method in class woSource.math.ImgProc

WO 3/29/08 my version computes essentially the cross-sectional area which is more robust than the 1D closest point in the version below

only computes distance at one point = the seed point
7/2/2012 this is messed up since a true distance would have to be float.

distAd - Variable in class woSource.VesselSegm

distanceToSnake(Point2D) - Method in class woSource.InteractiveSnake.SmoothSnake

find closest smooth-snake point distance.

distMap - Variable in class woSource.PulmonaryTrunkSegm

distTransform_mm(boolean[][][], float, float) - Static method in class woSource.math.ImgProc

WO 8/22/2012 version to compute in mm

distTransformIsoVoxels(boolean[][][]) - Static method in class woSource.math.ImgProc

3D distance transform from http://www.pvv.org/~perchrh/imagej/DT3D_.java gives only integeter outcomes so is not a true Eudlidan distance.

divide(short[][], int) - Static method in class woSource.math.ArraysI

matrix multiplication by 1/scalar

divide(short[][][], int) - Static method in class woSource.math.ArraysI

matrix multiplication by 1/scalar

divide(short[][][][], int) - Static method in class woSource.math.ArraysI

divide(int[][], int) - Static method in class woSource.math.ArraysI

divide(int[][][], int) - Static method in class woSource.math.ArraysI

divide(int[][][][], int) - Static method in class woSource.math.ArraysI

doDilate(boolean[][][], float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

10/4/2012 intent is to invoke this through the parallel version.

doEdgePtsOnly - Variable in class woSource.noduleDetectionModule

doErode(boolean[][][], float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

10/4/2012 intent is to run this through the parallel version

doFloodFill - Variable in class woSource.seededRegionGrowing

DoFullyManual - Variable in class woSource.InteractiveSnake

doingConsVsTags - Variable in class woSource.HeartSegm

doInteractive - Variable in class woSource.lungSnake

doManualLungSeg() - Method in class woSource.humanLungSegm

doManualLungSeg() - Method in class woSource.noduleDetection

doManualLungSegm - Variable in class woSource.humanLungSegm

doNCCCopt(String) - Method in class woSource.noduleDetection

doNCCCopt(String) - Method in class woSource.noduleDetectionModule

doOpt(boolean) - Method in class woSource.ImageRegistrationPS

doOutsideRoiFill(boolean[][], Rectangle) - Static method in class woSource.math.ImgProc

doOutsideRoiFill(byte[][], Rectangle, byte) - Static method in class woSource.math.ImgProc

doOutsideRoiFill(short[][], Rectangle, short) - Static method in class woSource.math.ImgProc

doOutsideRoiFill(boolean[][][], Rectangle3D) - Static method in class woSource.math.ImgProc

doOutsideRoiFill(byte[][][], Rectangle3D, byte) - Static method in class woSource.math.ImgProc

doOutsideRoiFill(short[][][], Rectangle3D, short) - Static method in class woSource.math.ImgProc

doreg(ImagePlus, ImagePlus) - Method in class woSource.ImgRegistration

doreg(ImagePlus, short[][][], ImagePlus, short[][][]) - Method in class woSource.ImgRegistration

doreg(ImagePlus, short[][][], Rectangle3D, ImagePlus, short[][][], Rectangle3D) - Method in class woSource.ImgRegistration

doRunGUI - Variable in class woSource.humanLungSegm

DoseCalc - Class in woSource

DoseCalc() - Constructor for class woSource.DoseCalc

doseDepths - Variable in class woSource.DoseReader

doseDepths - Variable in class woSource.DoseReader_Oct2012_oldUR

doseGridScalingFactor - Variable in class woSource.DoseReader

doseHeights - Variable in class woSource.DoseReader

doseHeights - Variable in class woSource.DoseReader_Oct2012_oldUR

doseImgTopLeft - Variable in class woSource.DoseReader

doseImgXdir - Variable in class woSource.DoseReader

doseImgYdir - Variable in class woSource.DoseReader

doseImgZdir - Variable in class woSource.DoseReader

DoseReader - Class in woSource

DoseReader(String) - Constructor for class woSource.DoseReader

DoseReader() - Constructor for class woSource.DoseReader

DoseReader_Oct2012_oldUR - Class in woSource

DoseReader_Oct2012_oldUR(String) - Constructor for class woSource.DoseReader_Oct2012_oldUR

DoseReader_Oct2012_oldUR() - Constructor for class woSource.DoseReader_Oct2012_oldUR

doseRect - Variable in class woSource.DoseReader

doseRect - Variable in class woSource.DoseReader_Oct2012_oldUR

doseValues - Variable in class woSource.DoseReader

doseValues - Variable in class woSource.DoseReader_Oct2012_oldUR

DoseVolumeStats - Class in woSource

DoseVolumeStats() - Constructor for class woSource.DoseVolumeStats

DoseVsIntensity - Class in woSource

DoseVsIntensity() - Constructor for class woSource.DoseVsIntensity

doseWidths - Variable in class woSource.DoseReader

doseWidths - Variable in class woSource.DoseReader_Oct2012_oldUR

doSnakeLungSegm() - Method in class woSource.humanLungSegm

doSnakesOnPrevMasks - Variable in class woSource.humanLungSegm

dot(float[], float[]) - Static method in class woSource.math.MathII

vector dot-product.

dot(double[], double[]) - Static method in class woSource.math.MathII

dot(Point2D, Point2D) - Static method in class woSource.math.MathII

dot(Point3D, Point3D) - Static method in class woSource.math.MathII

doTraversal() - Method in class woSource.PulmonaryTrunkSegm

doubleFactorial(int) - Static method in class woSource.math.MathI

draw(Graphics, ImageCanvas) - Method in class woSource.FEelemClass

draw(Graphics, ImageCanvas) - Method in class woSource.FEmeshClass

draw(Graphics, ImageCanvas) - Method in class woSource.FEnodeClass

Draw(Graphics, ScreenSelectorCanvas) - Method in class woSource.InteractiveSnake.Candidates

Draw(Graphics, ImageCanvas) - Method in class woSource.InteractiveSnake.Candidates

Draw(Graphics, ImageCanvas) - Method in class woSource.InteractiveSnake.SmoothSnake

Draw(Graphics, ImageCanvas, Color) - Method in class woSource.InteractiveSnake.SmoothSnake

Draw(Graphics, ScreenSelectorCanvas) - Method in class woSource.InteractiveSnake.SmoothSnake

Draw(ArrayDisplay) - Method in class woSource.InteractiveSnake.Snake

11/6/2014 roi's draw well but my snakes disappear while adjusting or when done.

Draw(ArrayDisplay, Color) - Method in class woSource.InteractiveSnake.Snake

Draw(Graphics, ImageCanvas) - Method in class woSource.InteractiveSnake.Snake

Draw(Graphics, ImageCanvas, Color) - Method in class woSource.InteractiveSnake.Snake

Draw(ArrayDisplay) - Method in class woSource.InteractiveSnake.SnakeStack

Draw(ArrayDisplay) - Method in class woSource.math.VesselBranch

Draw(ArrayDisplay, boolean) - Method in class woSource.math.VesselBranch

Draw(ArrayDisplay, boolean, int) - Method in class woSource.math.VesselBranch

Draw(ArrayDisplay) - Method in class woSource.math.VesselTree

Draw(ArrayDisplay, boolean) - Method in class woSource.math.VesselTree

Draw() - Method in class woSource.VesselSegm

Draw(ArrayDisplay) - Method in class woSource.VesselSegm

Draw(boolean) - Method in class woSource.VesselSegm

Draw(ArrayDisplay, boolean) - Method in class woSource.VesselSegm

Draw3D(Graphics, ScreenSelectorCanvas, double[][]) - Method in class woSource.InteractiveSnake.Snake

DrawContour(Graphics, ImageCanvas, int, float, float, float, float, int, int) - Method in class woSource.DVHCalc

DrawContour(Graphics, ImageCanvas, int) - Method in class woSource.DVHCalc

DrawNearestContour(Graphics, ImageCanvas, float, float, float, float, float, int, int) - Method in class woSource.DVHCalc

drawOnArrayDisplay() - Method in class woSource.Point3Dviewer

dsvbksb(double[][], double[], double[][], int, int, double[]) - Static method in class woSource.math.OptMath

dsvdcmp(double[][], int, int, double[], double[][]) - Static method in class woSource.math.OptMath

DTIanalysis - Class in woSource

DTIanalysis() - Constructor for class woSource.DTIanalysis

Duplicate(ArrayDisplay) - Method in class woSource.math.ArrayDisplay

Duplicate() - Method in class woSource.math.VesselTree

DVHCalc - Class in woSource

DVHCalc(float[], float[], float[], float[][][], ArrayDisplay) - Constructor for class woSource.DVHCalc

E

EAST - Variable in class woSource.GenericRecallableDialog

edgeFill(boolean[][]) - Static method in class woSource.math.ImgProc

WO boolean version 1/10/2012
Nearly always faster to first find bounding rect then process over only the Roi.

edgeFill(boolean[][], int) - Static method in class woSource.math.ImgProc

edgeFill(boolean[][], Rectangle) - Static method in class woSource.math.ImgProc

edgeFill(boolean[][], Rectangle, int) - Static method in class woSource.math.ImgProc

edgeFill(byte[][]) - Static method in class woSource.math.ImgProc

edgeFill(byte[][], Rectangle) - Static method in class woSource.math.ImgProc

edgeFill(byte[][], int) - Static method in class woSource.math.ImgProc

edgeFill(byte[][], Rectangle, byte, int) - Static method in class woSource.math.ImgProc

edgeFill(short[][]) - Static method in class woSource.math.ImgProc

edgeFill(short[][], Rectangle) - Static method in class woSource.math.ImgProc

edgeFill(short[][], int) - Static method in class woSource.math.ImgProc

edgeFill(short[][], Rectangle, short, int) - Static method in class woSource.math.ImgProc

edgeFill(byte[][][], int, int) - Static method in class woSource.math.ImgProc

does not include sliceEnd (< not <=) 10/17/2013 want to comppute edgefill only over usable portion of image.

edgeFill(byte[][][], int, int, int) - Static method in class woSource.math.ImgProc

edgeFill(byte[][][]) - Static method in class woSource.math.ImgProc

WO 3/4/11 modified to run in //

edgeFill(byte[][][], int) - Static method in class woSource.math.ImgProc

edgeFill(boolean[][][], int, int) - Static method in class woSource.math.ImgProc

WO 1/10/2012 boolean version does not include sliceEnd (< not <=)
note that this acts on each 2D slice independently (for //-ization) so not a true 3D fill.

edgeFill(boolean[][][], int, int, int) - Static method in class woSource.math.ImgProc

edgeFill(boolean[][][]) - Static method in class woSource.math.ImgProc

WO 3/4/11 modified to run in // as sets of 2D edgefills

edgeFill(boolean[][][], int) - Static method in class woSource.math.ImgProc

edgeFill3D(boolean[][][]) - Static method in class woSource.math.ImgProc

WO 9/26/2012 true 3D version

edgeFill3D(boolean[][][], Rectangle3D, int) - Static method in class woSource.math.ImgProc

edgeFill3D(byte[][][]) - Static method in class woSource.math.ImgProc

edgeFill3D(byte[][][], int) - Static method in class woSource.math.ImgProc

edgeFill3D(byte[][][], Rectangle3D, byte, int) - Static method in class woSource.math.ImgProc

edgeFill3D(short[][][]) - Static method in class woSource.math.ImgProc

edgeFill3D(short[][][], Rectangle3D, short, int) - Static method in class woSource.math.ImgProc

EdgeFillThread(byte[][][], int, int) - Constructor for class woSource.math.ImgProc.EdgeFillThread

EdgeFillThread(byte[][][], int, int, int) - Constructor for class woSource.math.ImgProc.EdgeFillThread

EdgeFillThread(boolean[][][], int, int) - Constructor for class woSource.math.ImgProc.EdgeFillThread

EdgeFillThread(boolean[][][], int, int, int) - Constructor for class woSource.math.ImgProc.EdgeFillThread

edgeFinder(byte[][]) - Static method in class woSource.math.ImgProc

edgeFinder(byte[][][]) - Static method in class woSource.math.ImgProc

edgeFinder(short[][]) - Static method in class woSource.math.ImgProc

edgeFinder(short[][][]) - Static method in class woSource.math.ImgProc

edgeFinder(float[][]) - Static method in class woSource.math.ImgProc

edgeFinder(float[][][]) - Static method in class woSource.math.ImgProc

edgeFinderReplaceA(byte[][]) - Static method in class woSource.math.ImgProc

edge finding algo: threshold; open; close; fill outside; gradient

edgeFinderReplaceA(byte[][][]) - Static method in class woSource.math.ImgProc

edgePtsImage - Variable in class woSource.noduleDetectionModule

elementLength - Variable in class woSource.DicomAnon

ElemNodes - Variable in class woSource.FEelemClass

Elems - Variable in class woSource.FEmeshClass

ElemScales - Variable in class woSource.FEelemClass

enableButton(int) - Method in class woSource.GenericRecallableDialog

enableCreateMaskSaveAsDicom - Variable in class woSource.InteractiveSnake

enableCrop - Variable in class woSource.AirwaySegm

endepichoices - Variable in class woSource.HeartSegm

endIndices - Variable in class woSource.lungSnake

endPt - Variable in class woSource.InteractiveSnake.Snake

endpts - Variable in class woSource.lungSnake

Energy_Bend - Variable in class woSource.InteractiveSnake.Snake

Energy_Pressure - Variable in class woSource.InteractiveSnake.Snake

Energy_Stretch - Variable in class woSource.InteractiveSnake.Snake

equals(Complex) - Method in class woSource.math.Complex

equalsWithinLimits(Complex, double) - Method in class woSource.math.Complex

erode(byte[][], int) - Static method in class woSource.math.ImgProc

erosion: turn OFF if any pixels in region are OFF

erode(byte[][], int, Rectangle) - Static method in class woSource.math.ImgProc

erode(byte[][], float) - Static method in class woSource.math.ImgProc

erode(byte[][], float, Rectangle) - Static method in class woSource.math.ImgProc

erode(boolean[][], int) - Static method in class woSource.math.ImgProc

erode(boolean[][], int, Rectangle) - Static method in class woSource.math.ImgProc

erode(boolean[][], float) - Static method in class woSource.math.ImgProc

erode(boolean[][], float, Rectangle) - Static method in class woSource.math.ImgProc

erode(byte[][][], int) - Static method in class woSource.math.ImgProc

erode(byte[][][], float) - Static method in class woSource.math.ImgProc

erode(byte[][][], int, float) - Static method in class woSource.math.ImgProc

erode(byte[][][], float, float) - Static method in class woSource.math.ImgProc

erode(byte[][][], int, Rectangle3D) - Static method in class woSource.math.ImgProc

erode(byte[][][], float, Rectangle3D) - Static method in class woSource.math.ImgProc

erode(byte[][][], int, float, Rectangle3D) - Static method in class woSource.math.ImgProc

10/19/11 WO in 2004 had problem of wrap-around in slice(Z) direction.

erode(byte[][][], float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

erode(boolean[][][], int) - Static method in class woSource.math.ImgProc

erode(boolean[][][], float) - Static method in class woSource.math.ImgProc

erode(boolean[][][], int, float) - Static method in class woSource.math.ImgProc

erode(boolean[][][], float, float) - Static method in class woSource.math.ImgProc

erode(boolean[][][], int, Rectangle3D) - Static method in class woSource.math.ImgProc

erode(boolean[][][], float, Rectangle3D) - Static method in class woSource.math.ImgProc

erode(boolean[][][], int, float, Rectangle3D) - Static method in class woSource.math.ImgProc

10/19/11 WO in 2004 had problem of wrap-around in slice(Z) direction.

erode(boolean[][][], float, float, boolean[][][]) - Static method in class woSource.math.ImgProc

WO 7/3/2012 version where you pass in all the points at the edge that matter for eroding

erode(boolean[][][], float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

WO 10/3/2012 parallel version.

erodeDilateOpRad - Variable in class woSource.humanLungSegm

erodeGray(byte[][], boolean[][]) - Static method in class woSource.math.ImgProc

erodeGray(byte[][][], boolean[][]) - Static method in class woSource.math.ImgProc

erodeGray(short[][], boolean[][]) - Static method in class woSource.math.ImgProc

erodeGray(short[][][], boolean[][]) - Static method in class woSource.math.ImgProc

ErodeThread(boolean[][][], float, float, Rectangle3D) - Constructor for class woSource.math.ImgProc.ErodeThread

ErosionRadius - Variable in class woSource.AirwaySegm

ErosionRadius - Variable in class woSource.PulmonaryTrunkSegm

eval_Hermite(float, float, float, float, float) - Static method in class woSource.math.MathII

eval_Hermite(double, double, double, double, double) - Static method in class woSource.math.MathII

exp() - Method in class woSource.math.Complex

exp(Complex) - Static method in class woSource.math.Complex

exp(double) - Static method in class woSource.math.Complex

exp(double) - Static method in class woSource.math.MathI

exp(float) - Static method in class woSource.math.MathI

expMinusJayArg(double) - Static method in class woSource.math.Complex

expPlusJayArg(double) - Static method in class woSource.math.Complex

exsec() - Method in class woSource.math.Complex

exsec(Complex) - Static method in class woSource.math.Complex

extend(byte[], int) - Static method in class woSource.math.ArraysI

extend(byte[][], int) - Static method in class woSource.math.ArraysI

extend(byte[][], int, int) - Static method in class woSource.math.ArraysI

extend(byte[][][], int) - Static method in class woSource.math.ArraysI

extend(byte[][][], int, int, int) - Static method in class woSource.math.ArraysI

extend(int[], int) - Static method in class woSource.math.ArraysI

extend(float[], int) - Static method in class woSource.math.ArraysI

extend(double[], int) - Static method in class woSource.math.ArraysI

extend(Point2D[], int) - Static method in class woSource.math.ArraysI

extend(Point3D[], int) - Static method in class woSource.math.ArraysI

extend(Point3Dint[], int) - Static method in class woSource.math.ArraysI

extend(short[][], int) - Static method in class woSource.math.ArraysI

extend(short[][], int, int) - Static method in class woSource.math.ArraysI

extend(short[][][], int) - Static method in class woSource.math.ArraysI

extend(short[][][], int, int, int) - Static method in class woSource.math.ArraysI

extend(short[][][][], int) - Static method in class woSource.math.ArraysI

extend(short[][][][], int, int, int, int) - Static method in class woSource.math.ArraysI

extend(int[][], int) - Static method in class woSource.math.ArraysI

extend(int[][], int, int) - Static method in class woSource.math.ArraysI

extend(int[][][], int) - Static method in class woSource.math.ArraysI

extend(int[][][], int, int, int) - Static method in class woSource.math.ArraysI

extend(int[][][][], int) - Static method in class woSource.math.ArraysI

extend(int[][][][], int, int, int, int) - Static method in class woSource.math.ArraysI

extend(float[][], int) - Static method in class woSource.math.ArraysI

extend(float[][], int, int) - Static method in class woSource.math.ArraysI

extend(Point2D[][], int) - Static method in class woSource.math.ArraysI

extend(Point2D[][], int, int) - Static method in class woSource.math.ArraysI

extend(Point3D[][], int, int) - Static method in class woSource.math.ArraysI

extend(Point3Dint[][], int, int) - Static method in class woSource.math.ArraysI

extend(float[][][], int) - Static method in class woSource.math.ArraysI

extend(float[][][], int, int, int) - Static method in class woSource.math.ArraysI

extend(float[][][][], int) - Static method in class woSource.math.ArraysI

extend(float[][][][], int, int, int, int) - Static method in class woSource.math.ArraysI

extend(float[][][][][], int) - Static method in class woSource.math.ArraysI

extend(float[][][][][], int, int, int, int, int) - Static method in class woSource.math.ArraysI

extend(float[][][][][][], int) - Static method in class woSource.math.ArraysI

extend(float[][][][][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

extend(HyperSkelPair[], int) - Static method in class woSource.math.ArraysI

extend(int) - Method in class woSource.math.VesselBranch

extend(int) - Method in class woSource.math.VesselTree

extendBranchEnds() - Method in class woSource.VesselSegm

attempt to fix error of skeletonization routine that cuts each branch short at the ends
Requires characterized branch tree and object mask.

extendPtsArrays() - Method in class woSource.InteractiveSnake.Snake

intended for when need to increase the NPTs above NMAX

F

f - Variable in class woSource.DicomAnon

factoral(int) - Static method in class woSource.math.MathI

farthestMaxpt(float[][], Point2D) - Static method in class woSource.math.ArraysI

WO 6/30/11 find max point.

farthestMaxpt(float[][], Point2D, int, int, int, int) - Static method in class woSource.math.ArraysI

fastApproxNCCC(short[][][], float[][][][]) - Static method in class woSource.math.ImgProc

WO 1/4/11 fast but approximate NCCC calc based on Matlab's normxcorr3
assumes all the kernals in this stack are the same size.

fastMarching(byte[][][], int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

WO 5/18/2012 difference between fast marching and floodfill(=region growing) is fast marching computes a threshold for inclusion on the fly, and keeps track of the wavefront location.

fastMarching(short[][][], int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

fastNMI(short[][][], short[][][], int, int, int) - Static method in class woSource.math.ImgProc

fastNMI(short[][][], short[][][], int[], int[], double, int, int, int) - Static method in class woSource.math.ImgProc

FEelemClass - Class in woSource

FEelemClass(String) - Constructor for class woSource.FEelemClass

FEmeshClass - Class in woSource

FEmeshClass(String, int, int) - Constructor for class woSource.FEmeshClass

FEnodeClass - Class in woSource

FEnodeClass(String) - Constructor for class woSource.FEnodeClass

fifthrt(double) - Static method in class woSource.math.MathI

fifthrt(float) - Static method in class woSource.math.MathI

fileName - Variable in class woSource.DicomAnon

fileName - Variable in class woSource.ImageRegistrationPS

fileName - Variable in class woSource.math.SimTagImageInfo

filename_addon - Variable in class woSource.InteractiveSnake

fillAContour(Graphics, ImageCanvas, int, float, float, float, float, int, int) - Method in class woSource.DVHCalc

fillBright - Variable in class woSource.seededRegionGrowing

fillContour(Graphics, ImageCanvas, float, float, float, float, float, int, int) - Method in class woSource.DVHCalc

fillInTags(byte[][], boolean, float) - Method in class woSource.HeartSegm

fillInTags(byte[][][], boolean, float) - Method in class woSource.HeartSegm

fillInTags(short[][], boolean, float) - Method in class woSource.HeartSegm

fillInTags(short[][][], boolean, float) - Method in class woSource.HeartSegm

fillInTransformedHoles(short[][]) - Static method in class woSource.math.ImgProc

idea is that in the transformation step above some pixels in defTransImg may not be mapped to a pixel in the original image and will have a value of '-1' (or -1042) this flag is used in the calculation of NCC nad NMI, however you can use this function to clean up the image for a pretty picture.

fillInTransformedHoles(short[][][]) - Static method in class woSource.math.ImgProc

idea is that in the transformation step above some pixels in defTransImg may not be mapped to a pixel in the original image and will have a value of '-1' (or -1042) this flag is used in the calculation of NCC nad NMI, however you can use this function to clean up the image for a pretty picture.

fillOuterContour(byte[][], Polygon2D) - Static method in class woSource.math.ImgProc

WO 12/7/09 want binary image of area inside and including contour

find_multiD_min(float[]) - Method in class woSource.math.OptMath

find_opt_state() - Method in class woSource.InteractiveSnake.Snake

find_opt_state(int) - Method in class woSource.InteractiveSnake.Snake

findBestFitEllipsoid(float[][]) - Method in class woSource.math.HeartLongAxis

findBottomWallLeftLung(int) - Method in class woSource.lungSnake

now find limits of outside lung wall.

findBottomWallLeftLung(int) - Method in class woSource.noduleDetection.lungSnake

findBottomWallRightLung(int) - Method in class woSource.lungSnake

findBottomWallRightLung(int) - Method in class woSource.noduleDetection.lungSnake

findClosestMark(int, float, float) - Method in class woSource.ImageReviewer

findClosestProjection(Point2D, int) - Method in class woSource.InteractiveSnake.Snake

find closest snake point along Normal lines.

findClosestProjection(Point2D, int) - Method in class woSource.InteractiveSnake.SnakeStack

findClosestSkeletonPt(Point3Dint) - Method in class woSource.VesselSegm

start by searching near seed point for best distance value

findClosestSkeletonPt(int, int, int) - Method in class woSource.VesselSegm

findEdgePts(int, boolean) - Method in class woSource.lungSnake

finds edges on lungMask along radial projections from centroid.

findEdgePts(int, boolean) - Method in class woSource.noduleDetection.lungSnake

findFarthestFalseConnection() - Method in class woSource.math.VesselTree

Intent is to find children whose angle from each other is large (>110 degrees) AND whose radius is larger than the parent.

findFarthestFalseConnection(boolean) - Method in class woSource.math.VesselTree

findfastNMImax(short[][][], short[][][]) - Static method in class woSource.math.ImgProc

findfastNMImax(short[][][], short[][][], int, int, int) - Static method in class woSource.math.ImgProc

findLocalExtrema(short[][], int) - Static method in class woSource.math.ArraysI

returns Point2D array of length of number of good candidates, up to NMax

findLocalExtrema(short[][], int, int) - Static method in class woSource.math.ArraysI

findLocalExtrema(short[][], int, float) - Static method in class woSource.math.ArraysI

findLocalExtrema(short[][], int, float, float, int) - Static method in class woSource.math.ArraysI

findLocalExtrema(short[][][], int, float, int) - Static method in class woSource.math.ArraysI

WO 2/16/11 omitted DivotThresh as doesn't make sense with NCCC calculations

findLocalExtrema(byte[][][], int, int, int) - Static method in class woSource.math.ArraysI

WO 1/19/11 3D version; 2/16/11 removing divotThreshold, and corrected error where if a new close point was found, it didn't check to see if the old point was worse and throw it out if so.

findLocalExtrema(byte[][][], int, int, int, int, int) - Static method in class woSource.math.ArraysI

findLocalExtrema(byte[][][][], int, int, int) - Static method in class woSource.math.ArraysI

WO 12/23/10 for stack of images

findLocalExtrema(byte[][][][], int, int, int, int, int) - Static method in class woSource.math.ArraysI

WO 12/23/10 for stack of images with same search size for each

findLocalExtrema(short[][][][], int, short, int) - Static method in class woSource.math.ArraysI

findLocalExtrema(int[][], int) - Static method in class woSource.math.ArraysI

findLocalExtrema(int[][], int, int) - Static method in class woSource.math.ArraysI

findLocalExtrema(int[][], int, float) - Static method in class woSource.math.ArraysI

findLocalExtrema(int[][], int, float, float, int) - Static method in class woSource.math.ArraysI

findNMImax(short[][][], short[][][], int, int, int) - Static method in class woSource.math.ImgProc

find max NMI point, given the starting location (az,ax,ay) -- thus is doing a minor attempt at registration
assume monotonic neighborhood

findOptKmeansBinsStarts(int[], int) - Static method in class woSource.math.ImgProc

returns binCentroids (!= bin centers -- allow for nonsymmetric bins)

findSkeletonTop(Point3Dint, int) - Method in class woSource.VesselSegm

3/22/2013 after plugging all of the false connections between trees with calls to splitTreeAtConnection() we want to generate updated masks for each tree to enable colored display in MIPsColor.

findSkeletonTop(int, int, int, int) - Method in class woSource.VesselSegm

findSkeletonTopTry(Point3Dint, int) - Method in class woSource.VesselSegm

findSkeletonTopTry(Point3Dint, int, boolean, boolean) - Method in class woSource.VesselSegm

findSkeletonTopTry(int, int, int, int) - Method in class woSource.VesselSegm

WO 7/17/2012 this is working correctly for 2D test image, but fails usually for human 3D pulmonary tree and for the colon.

findSkeletonTopTry(int, int, int, int, boolean, boolean) - Method in class woSource.VesselSegm

findStartingIndex(int, boolean) - Method in class woSource.lungSnake

define global startI used by findBottomWallLeft() and findTopWallLeft()

findStartingIndex(int, boolean) - Method in class woSource.noduleDetection.lungSnake

findTopWallEnd(int, double, boolean) - Method in class woSource.lungSnake

findTopWallEnd(int, double, boolean) - Method in class woSource.noduleDetection.lungSnake

fineThresh - Variable in class woSource.noduleDetectionModule

finishReg(Properties[]) - Method in class woSource.ImageRegistration

WO 9/13/10 when done want to clear all the windows and the gui, but save the deformed floating images as an open window that the function that called this can continue to use.

firstPassThresh - Variable in class woSource.noduleDetectionModule

firstSAconIndex - Variable in class woSource.HeartSegm

fit_vol_area_calc - Class in woSource

fit_vol_area_calc() - Constructor for class woSource.fit_vol_area_calc

fitCoeffs - Variable in class woSource.ContourFit

fitDoseCoeffs() - Method in class woSource.DoseReader

fit the 3D dose field to a spherical harmonic like series, probably intended to help create synthetic dose- response image set for testing and validation

fitDoseCoeffs() - Method in class woSource.DoseReader_Oct2012_oldUR

fittedBifurCenterlinePts_mm - Variable in class woSource.math.VesselBranch

fittedCoeffs - Variable in class woSource.DoseReader

fittingOrder - Variable in class woSource.ContourFit

fixedSnakeEnds - Variable in class woSource.InteractiveSnake.SmoothSnake

FixEndPoints(Point2D, Point2D) - Method in class woSource.InteractiveSnake.Snake

flipDepth() - Method in class woSource.DoseReader

flipDepth() - Method in class woSource.DoseReader_Oct2012_oldUR

flipHeight() - Method in class woSource.DoseReader

flipHeight() - Method in class woSource.DoseReader_Oct2012_oldUR

flipLR(byte[][]) - Static method in class woSource.math.ArraysI

meant to flip an image horizontally (Left-right)

flipLR(short[][]) - Static method in class woSource.math.ArraysI

flipLR(float[][]) - Static method in class woSource.math.ArraysI

flipWidth() - Method in class woSource.DoseReader

flipWidth() - Method in class woSource.DoseReader_Oct2012_oldUR

floodFill(boolean[][], int, int) - Static method in class woSource.math.ImgProc

fill image starting from seed point.

floodFill(boolean[][], int, int, int) - Static method in class woSource.math.ImgProc

floodFill(boolean[][], int, int, Rectangle) - Static method in class woSource.math.ImgProc

floodFill(boolean[][], int, int, Rectangle, int) - Static method in class woSource.math.ImgProc

floodFill(byte[][], int, int) - Static method in class woSource.math.ImgProc

WO the original, byte version

floodFill(byte[][], int, int, int) - Static method in class woSource.math.ImgProc

floodFill(byte[][], int, int, byte) - Static method in class woSource.math.ImgProc

floodFill(byte[][], int, int, Rectangle) - Static method in class woSource.math.ImgProc

floodFill(byte[][], int, int, Rectangle, int) - Static method in class woSource.math.ImgProc

floodFill(byte[][], int, int, Rectangle, byte, int) - Static method in class woSource.math.ImgProc

floodFill(short[][], int, int) - Static method in class woSource.math.ImgProc

floodFill(short[][], int, int, int) - Static method in class woSource.math.ImgProc

floodFill(short[][], int, int, short) - Static method in class woSource.math.ImgProc

floodFill(short[][], int, int, Rectangle) - Static method in class woSource.math.ImgProc

floodFill(short[][], int, int, Rectangle, int) - Static method in class woSource.math.ImgProc

floodFill(short[][], int, int, Rectangle, short, int) - Static method in class woSource.math.ImgProc

floodFill(boolean[][][], int, int, int) - Static method in class woSource.math.ImgProc

7/31/2012 boolean 3D version.

floodFill(boolean[][][], int, int, int, Rectangle3D) - Static method in class woSource.math.ImgProc

floodFill(boolean[][][], int, int, int, int) - Static method in class woSource.math.ImgProc

floodFill(boolean[][][], int, int, int, Rectangle3D, int) - Static method in class woSource.math.ImgProc

floodFill(boolean[][][], int, int, int, boolean) - Static method in class woSource.math.ImgProc

floodFill(boolean[][][], int, int, int, Rectangle3D, boolean) - Static method in class woSource.math.ImgProc

floodFill(boolean[][][], int, int, int, int, boolean) - Static method in class woSource.math.ImgProc

floodFill(boolean[][][], int, int, int, Rectangle3D, int, boolean) - Static method in class woSource.math.ImgProc

WO 4/15/08 passing fillval of 0 interpreted as flag to do labeled version

floodFill(byte[][][], int, int, int) - Static method in class woSource.math.ImgProc

This is equivalent to seeded region growing but where the fill occurs only to zero-valued pixels.

floodFill(byte[][][], int, int, int, byte) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, Rectangle3D) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, Rectangle3D, byte) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, int) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, byte, int) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, Rectangle3D, int) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, Rectangle3D, byte, int) - Static method in class woSource.math.ImgProc

WO 4/15/08 passing fillval of 0 interpreted as flag to do labeled version

floodFill(byte[][][], int, int, int, float) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, byte, float) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, Rectangle3D, float) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, Rectangle3D, byte, float) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, int, float) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, byte, int, float) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, Rectangle3D, int, float) - Static method in class woSource.math.ImgProc

floodFill(byte[][][], int, int, int, Rectangle3D, byte, int, float) - Static method in class woSource.math.ImgProc

WO 4/15/08 passing fillval of 0 interpreted as flag to do labeled version

floodFill(short[][][], int, int, int) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, short) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, Rectangle3D) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, Rectangle3D, short) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, int) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, short, int) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, Rectangle3D, int) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, Rectangle3D, short, int) - Static method in class woSource.math.ImgProc

WO 4/15/08 passing fillval of 0 interpreted as flag to do labeled version

floodFill(short[][][], int, int, int, float) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, short, float) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, Rectangle3D, float) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, Rectangle3D, short, float) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, int, float) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, short, int, float) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, Rectangle3D, int, float) - Static method in class woSource.math.ImgProc

floodFill(short[][][], int, int, int, Rectangle3D, short, int, float) - Static method in class woSource.math.ImgProc

This is equivalent to seeded region growing but where the fill occurs only to zero-valued pixels.

floodFillDownward(byte[][][], int, int, int) - Static method in class woSource.math.ImgProc

WO 8/26/11 goal to pre-process downward flood fill set to avoid linking downward when there is only a single pixel connection in neighborhood, to omit bowels from lung segmentation.

floodFillInitialDownward(short[][][], int, int, int, short, float) - Static method in class woSource.math.ImgProc

floodFillInitialUpward(byte[][][], int, int, int, byte, float) - Static method in class woSource.math.ImgProc

WO 11/27/2015 goal to initially flood only upward to avoid things like the LV/RV from the aortic root, but allow the fill to eventually go downward (i.e.

floodFillInitialUpward(short[][][], int, int, int, short, float) - Static method in class woSource.math.ImgProc

floodfillMaskFromTop() - Method in class woSource.math.VesselTree

12/24/2012 intent is for after adding diskOntoMask or after split tree into 2 sub-trees, then need to regenerate the tree masks.

floodFillNlabel(byte[][][], int, int, int, int) - Static method in class woSource.math.ImgProc

WO 4/10/08 same as above except add parameter counting the flood layers and use as fillvalue

floodFillNlabel(byte[][][], int, int, int, Rectangle3D, int) - Static method in class woSource.math.ImgProc

focalLength - Variable in class woSource.math.HeartLongAxis

focusGained(FocusEvent) - Method in class woSource.ScreenSelectorCanvas

focusLost(FocusEvent) - Method in class woSource.ScreenSelectorCanvas

forwardTraceToLargestBranch(int, int) - Method in class woSource.VesselSegm

forwardTraceToLargeTerminusBranch(int, int) - Method in class woSource.VesselSegm

forwardTraceToTreeTop(int, int) - Method in class woSource.VesselSegm

foundedge - Variable in class woSource.lungSnake

four1(float[], int, int) - Static method in class woSource.math.MathII

(C) Copr.

fourier_eval(int, double) - Static method in class woSource.math.MathII

note that Num.

fourthrt(double) - Static method in class woSource.math.MathI

fourthrt(float) - Static method in class woSource.math.MathI

fromString(String) - Method in class woSource.math.LIDCnodule

fromString(String) - Method in class woSource.math.NoduleCandidate

FTshift(short[][]) - Static method in class woSource.math.MathII

WO 1/5/11 after performing an FT-InvFT calculation the image is out of order and needs the equivalent of Matlab's fftshift function

FTshift(short[][][]) - Static method in class woSource.math.MathII

FTshift(float[][]) - Static method in class woSource.math.MathII

FTshift(float[][][]) - Static method in class woSource.math.MathII

G

gasdev(Random) - Static method in class woSource.math.MathII

gaussianGradKernel(int) - Static method in class woSource.math.MathII

gaussianKernel(int) - Static method in class woSource.math.MathII

generic-sized gaussian kernel, symmetric
note: if passing an integer value, code assumes that n represents the pixel dimension of the resulting kernel; n should be odd so that the kernel is centered around the origin; and sigma = (n-1)/6
if passing a float value sigma, the pixel dimension is set to match 6 sigma

gaussianKernel(int, int) - Static method in class woSource.math.MathII

gaussianKernel(float) - Static method in class woSource.math.MathII

gaussianKernel(float, float) - Static method in class woSource.math.MathII

gaussianKernel(int, int, int) - Static method in class woSource.math.MathII

elliptical 3D gaussian kernel
uses ArrayDisplay indexing conventions A[depth][width][height]

gaussianKernel(double, double, double) - Static method in class woSource.math.MathII

gaussianKernel(float, float, float) - Static method in class woSource.math.MathII

gd - Variable in class woSource.MIPSviewer

gd - Variable in class woSource.Point3Dviewer

gd - Variable in class woSource.WindowLevelAdjuster

GenericRecallableDialog - Class in woSource

create a GenericDialog that remains active to allow for repeated runs through target program, enabling the use of add-on buttons to perform different and repeatable functions.

GenericRecallableDialog(String) - Constructor for class woSource.GenericRecallableDialog

GenericRecallableDialog(String, Frame) - Constructor for class woSource.GenericRecallableDialog

get2DRect() - Method in class woSource.math.Rectangle3D

get2ndHyperSkelPairIndex(int, int, int, int) - Method in class woSource.VesselSegm

get2ndHyperSkelPairIndex(Point3Dint, int) - Method in class woSource.VesselSegm

get3Dview() - Method in class woSource.ImageReviewer

get3DviewOfmark() - Method in class woSource.ImageReviewer

get3DviewOfNodule() - Method in class woSource.LIDCreview

get_parabolic_min(float, float, float, float, float, float) - Method in class woSource.math.OptMath

get_prosph_surf_terms(double, double, int) - Static method in class woSource.math.MathII

get_prosph_terms(double, double, double, int, double, int[], double[]) - Static method in class woSource.math.MathII

get_surfaceFitting_Nterms(int) - Static method in class woSource.math.MathII

getAdScreenHeight() - Method in class woSource.Point3Dviewer

getAlpha() - Method in class woSource.math.ArrayDisplay

getAmoebaCurValues() - Method in class woSource.ImageRegistration

getAncesterList(int) - Method in class woSource.math.VesselTree

7/8/2014 intent is to return a list of indices for the parent-ancesters of branch brat

getBendingAngle(int) - Method in class woSource.math.VesselBranch

getBifurcationCenterline(VesselBranch) - Method in class woSource.math.VesselBranch

goal to create the surface mesh that interpolates from the parent to this child.

getBinVariability(int[], float[], int) - Static method in class woSource.math.ImgProc

getBMcoeffs() - Method in class woSource.ImageRegistrationPS

getBoundingBox(boolean[][]) - Static method in class woSource.math.ImgProc

find boundaries of usable image

getBoundingBox(boolean[][], int) - Static method in class woSource.math.ImgProc

getBoundingBox(boolean[][][]) - Static method in class woSource.math.ImgProc

getBoundingBox(boolean[][][], int) - Static method in class woSource.math.ImgProc

getBoundingBox(boolean[][][], int, float) - Static method in class woSource.math.ImgProc

getBoundingBox(byte[][]) - Static method in class woSource.math.ImgProc

getBoundingBox(byte[][], int) - Static method in class woSource.math.ImgProc

getBoundingBox(byte[][][]) - Static method in class woSource.math.ImgProc

getBoundingBox(byte[][][], int) - Static method in class woSource.math.ImgProc

getBoundingBox(byte[][][], int, float) - Static method in class woSource.math.ImgProc

getBoundingBox(byte[][][], int, float, int) - Static method in class woSource.math.ImgProc

getBoundingBox(short[][]) - Static method in class woSource.math.ImgProc

getBoundingBox(short[][], int) - Static method in class woSource.math.ImgProc

getBoundingBox(short[][], int, int) - Static method in class woSource.math.ImgProc

getBoundingBox(short[][][]) - Static method in class woSource.math.ImgProc

getBoundingBox(short[][][], int) - Static method in class woSource.math.ImgProc

getBoundingBox(short[][][], int, float) - Static method in class woSource.math.ImgProc

getBoundingBox(short[][][], int, float, int) - Static method in class woSource.math.ImgProc

getBoundingBox(float[][]) - Static method in class woSource.math.ImgProc

getBoundingBox(float[][], int) - Static method in class woSource.math.ImgProc

getBoundingBox(Point3D[][]) - Static method in class woSource.math.ImgProc

getBoundingBox(Point3D[][], int) - Static method in class woSource.math.ImgProc

getBranchChildren(int) - Method in class woSource.math.VesselTree

getBranchNodeROI(int, int, int, int, int) - Method in class woSource.math.VesselTree

Intent is to create a mask that contains the region of influence for a given branch node over which to compute the correlation (NCCC) to the original image, for optimizing the nodal parameters.

getBranchNodeSimImage(int, int, Rectangle3D) - Method in class woSource.math.VesselTree

Intent is to create the similated vessel image only over the node of interest, over which to compute the correlation (NCCC) to the original image, for optimizing the nodal parameters.

getBranchWithStartLoc(int, int, int) - Method in class woSource.math.VesselTree

getButtonValue(int) - Method in class woSource.GenericRecallableDialog

Returns the contents of button 'i' field.

getChild1FrontVec(int, int) - Method in class woSource.VesselSegm

getChild1Index(int, int) - Method in class woSource.VesselSegm

getChild2FrontVec(int, int) - Method in class woSource.VesselSegm

getChild2Index(int, int) - Method in class woSource.VesselSegm

getChildrenBifurAngle(int, int) - Method in class woSource.VesselSegm

getChildrenIndices() - Method in class woSource.math.VesselBranch

getColor(String) - Method in class woSource.math.ArrayDisplay

getColor(String) - Static method in class woSource.math.MathI

getCount() - Method in class woSource.math.ImgProc.EdgeFillThread

getCurLevel() - Method in class woSource.AutoWindowLevel

getCurrentImageMatrix(boolean[][][]) - Static method in class woSource.math.ImgProc

Looks at the current highlighted window with an image and ROI and gets the dimensions and the image data into a 3d array option to use Roi to define image being retrieved
gets image matrix as [depth][width][height]

getCurrentImageMatrix(boolean[][][], ImagePlus) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(boolean[][][], boolean, ImagePlus) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(byte[][][]) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(byte[][][], boolean) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(byte[][][], ImagePlus) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(byte[][][], boolean, ImagePlus) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(short[][][]) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(short[][][], boolean) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(short[][][], ImagePlus) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(short[][][], boolean, ImagePlus) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(int[][][]) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(int[][][], boolean) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(float[][][]) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(float[][][], boolean, ImagePlus) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(byte[][]) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(byte[][], boolean) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(short[][]) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(short[][], boolean) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(int[][]) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(int[][], boolean) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(float[][]) - Static method in class woSource.math.ImgProc

getCurrentImageMatrix(float[][], boolean) - Static method in class woSource.math.ImgProc

getCurrentRoi() - Method in class woSource.InteractiveSnake.SnakeStack

getCurrentRoiRect() - Method in class woSource.InteractiveSnake.SnakeStack

getCurrentSlice() - Method in class woSource.math.ArrayDisplay

getCurrentSliceNumber() - Method in class woSource.math.ArrayDisplay

3/10/11 WO the cine image number from the DICOM "Image Number"

getCurrentSliceZ() - Method in class woSource.math.ArrayDisplay

3/10/11 WO the Z coord is now taken from the DICOM Image Position tag rather than the Slice Location tag because that is the value that the LIDC uses, and in many of the LIDC studies, these 2 values are not the same

getCurrentSnake() - Method in class woSource.InteractiveSnake.SnakeStack

getCursorLoc() - Method in class woSource.math.ArrayDisplay

WO 2/2/11 return the location of the cursor on the window

getCurValues() - Method in class woSource.ImageRegistration

getCurWindow() - Method in class woSource.AutoWindowLevel

getDefDoseBoundingRect() - Method in class woSource.DoseVsIntensity

getDeformedVoxelLocs(int) - Method in class woSource.ImageRegistrationPS

getDepth() - Method in class woSource.math.ArrayDisplay

getDicomInfo() - Method in class woSource.DicomAnon

getDicomPoint3D(ImagePlus, String) - Static method in class woSource.math.MathII

getDicomPoint3D(ImagePlus, String, int) - Static method in class woSource.math.MathII

getDicomValue(String, String) - Static method in class woSource.math.MathII

getDicomValue(String, String, String) - Static method in class woSource.math.MathII

getDicomValue(String, String, int) - Static method in class woSource.math.MathII

getDicomValue(String, String, int, String) - Static method in class woSource.math.MathII

WO 6/25/09 creating this intermediate before getStringString to check for dicom headers where we have found an extra ">Pixel Header" tag present, right before the real tag and with the '>' in front.

getDicomValue(ImagePlus, String) - Static method in class woSource.math.MathII

getDicomValue(ImagePlus, String, int) - Static method in class woSource.math.MathII

getDicomValue(Properties, String) - Static method in class woSource.math.MathII

getDicomValue(Properties, String, int) - Static method in class woSource.math.MathII

getDim(Object) - Static method in class woSource.math.ArraysI

getDisplay() - Method in class woSource.Deconvolver

getDistToCylAxis(float, float, float, float, float, float, float[], float, float, float) - Static method in class woSource.math.MathII

WO 3/18/2013 intent is for computing partial volume for pixels near a cylinder, want distance from the center of a voxel in space to the central axis of the cylinder along the shortest perpendicular.

getDistToCylAxis(float, float, float, float, float[], float, float) - Static method in class woSource.math.MathII

WO 3/18/2013 2D version of above.

getDrot() - Method in class woSource.ImageRegistration

getDrot() - Method in class woSource.ImgRegistration

getDscale() - Method in class woSource.ImageRegistration

getDscale() - Method in class woSource.ImgRegistration

getEdgeImage(boolean[][][]) - Static method in class woSource.math.ImgProc

getEdgeImage(boolean[][][], boolean) - Static method in class woSource.math.ImgProc

27 connections includes corners.

getEndVector() - Method in class woSource.math.VesselBranch

getEndVector(int) - Method in class woSource.math.VesselBranch

want unit vector[mm] pointing outward (toward children) from last point in branch that best fits through the last NvecPts(global, =5), for computing bifurcation angle.

getEquiBins(int[], int) - Static method in class woSource.math.ImgProc

returns array of bin starts[Nbins+1] where last element is end of array.

getFalse2DConnectionScore(int, int) - Method in class woSource.VesselSegm

getFalseLadderConnectionScore(int, int) - Method in class woSource.VesselSegm

getFarthestOnPtDist(boolean[][][], int, int, int, float) - Static method in class woSource.math.ImgProc

getFarthestOnPtDist(byte[][][], int, int, int, int, float) - Static method in class woSource.math.ImgProc

getFarthestOnPtDist(short[][][], int, int, int, int, float) - Static method in class woSource.math.ImgProc

getFFT_N(int) - Static method in class woSource.math.MathII

WO 5/22/01 want nearest integer N=2^m that is greater than n

getFileInfo() - Method in class woSource.DicomAnon

getFirstPoint() - Method in class woSource.math.VesselBranch

getFittedCenterlinePts_mm() - Method in class woSource.math.VesselTree

goal is to retrieve the fitted centerline points for all branches, including the bifurcation model from parent to child, to look for errors (bending) in the centerline fits.

getFocalLength() - Method in class woSource.math.HeartLongAxis

getFrontVector() - Method in class woSource.math.VesselBranch

getFrontVector(int) - Method in class woSource.math.VesselBranch

gives unit vector pointing distally down current branch from first point in branch that best fits through the first NvecPts(global, =5).

getGdScreenHeight() - Method in class woSource.Point3Dviewer

getGraphics() - Method in class woSource.math.ArrayDisplay

getHeaderInfo(float) - Method in class woSource.MIPSviewer

getHeartLAparams() - Method in class woSource.HeartSegm

getHeight() - Method in class woSource.math.ArrayDisplay

getHistogram(byte[]) - Static method in class woSource.math.ImgProc

getHistogram(byte[][]) - Static method in class woSource.math.ImgProc

getHistogram(byte[][][]) - Static method in class woSource.math.ImgProc

getHistogram(short[]) - Static method in class woSource.math.ImgProc

essentially scales image 0..255 then does histo analysis

getHistogram(short[][]) - Static method in class woSource.math.ImgProc

getHistogram(short[][], int) - Static method in class woSource.math.ImgProc

getHistogram(short[][][]) - Static method in class woSource.math.ImgProc

getHistogram(short[][][], int) - Static method in class woSource.math.ImgProc

getHistogram(ImagePlus, int) - Static method in class woSource.math.ImgProc

getHistogram(short[][][], short[][][]) - Static method in class woSource.math.ImgProc

2D histogram

getHistogram(short[][][], short[][][], int, int, int) - Static method in class woSource.math.ImgProc

get histogram in overlap region with center of B over pt (az,ax,ay) in A

getHrot() - Method in class woSource.ImageRegistration

getHrot() - Method in class woSource.ImgRegistration

getHscale() - Method in class woSource.ImageRegistration

getHscale() - Method in class woSource.ImgRegistration

getHyperSkelPairIndex(int, int, int) - Method in class woSource.VesselSegm

getHyperSkelPairIndex(Point3Dint) - Method in class woSource.VesselSegm

getHyperskelPairPt(int, int, int) - Method in class woSource.VesselSegm

getHyperskelPairPt(Point3Dint) - Method in class woSource.VesselSegm

getHyperskelPairPt(Point3Dint, int) - Method in class woSource.VesselSegm

getImag() - Method in class woSource.math.Complex

getImage() - Method in class woSource.math.SimTagImageInfo

getImage3Dcoords(short[][][], Properties[]) - Static method in class woSource.math.ImgProc

getImageCanvas() - Method in class woSource.math.ArrayDisplay

getImageData() - Method in class woSource.PetCTregistration

getImageJDataDir() - Static method in class woSource.math.ImgProc

getImageJOutputDir() - Static method in class woSource.math.ImgProc

getImageJOutputDir(FileInfo) - Static method in class woSource.math.ImgProc

getImageJOutputDir() - Method in class woSource.noduleDetection

getImagePlus() - Method in class woSource.math.ArrayDisplay

getImageProcessor() - Method in class woSource.math.ArrayDisplay

getImageProcessor(int) - Method in class woSource.math.ArrayDisplay

getImageProcessorStack() - Method in class woSource.math.ArrayDisplay

getImages() - Method in class woSource.math.SeriesImagesClass

getImageStack() - Method in class woSource.math.ArrayDisplay

getIndex() - Method in class woSource.math.VesselBranch

getInfOption() - Static method in class woSource.math.Complex

getInitView() - Method in class woSource.MIPSviewer

getInitView() - Method in class woSource.MIPSviewerColor

getInitView() - Method in class woSource.Point3Dviewer

getInterpolatedValue(byte[][], float, float) - Static method in class woSource.math.ArraysI

bi-linear interpolation of array elements

getInterpolatedValue(short[][], float, float) - Static method in class woSource.math.ArraysI

getInterpolatedValue(float[][], float, float) - Static method in class woSource.math.ArraysI

getInterpolatedValue(byte[][][], float, float, float) - Static method in class woSource.math.ArraysI

getInterpolatedValue(short[][][], float, float, float) - Static method in class woSource.math.ArraysI

getInvTransformedPtCoords_px(int, int, int) - Method in class woSource.ImageRegistration

inverse-transform the voxel dwh into the deformed coord system and return the sub-voxel coords dwh.

getInvTransformedPtCoords_px(float, float, float) - Method in class woSource.ImageRegistration

getInvTransformedPtCoords_px(int, int, int) - Method in class woSource.ImgRegistration

inverse-transform the voxel dwh into the deformed coord system and return the sub-voxel coords dwh.

getInvTransformedPtCoords_px(float, float, float) - Method in class woSource.ImgRegistration

getIPStack() - Method in class woSource.math.ArrayDisplay

getIsotropicSimImage(int, int, int) - Method in class woSource.math.VesselTree

getjori() - Static method in class woSource.math.Complex

getKmeansBins(int[], int) - Static method in class woSource.math.ImgProc

classic method bins pixels to nearest bin centers,.

getKmeansBins(int[], int, String) - Static method in class woSource.math.ImgProc

getKmeansBinsWO(int[], int) - Static method in class woSource.math.ImgProc

my version shifted bin sides around to min variance

getKmeansBinsWO(int[], int, String) - Static method in class woSource.math.ImgProc

getLabel() - Method in class woSource.math.ArrayDisplay

getLargestBranchLength() - Method in class woSource.math.VesselTree

getLargestBranchRadius() - Method in class woSource.math.VesselTree

getLargestChildRadius(int, int) - Method in class woSource.VesselSegm

getLargestParentSiblingRadius(int, int) - Method in class woSource.VesselSegm

GetLastEdgePts() - Method in class woSource.InteractiveSnake.Snake

getLastPoint() - Method in class woSource.math.VesselBranch

getLength() - Method in class woSource.InteractiveSnake.Snake

In pixel units

getLength() - Method in class woSource.math.VesselBranch

getLength_pixels() - Method in class woSource.math.VesselBranch

getLengthHistogram(int) - Method in class woSource.math.VesselTree

getLengthHistogram(int) - Method in class woSource.VesselSegm

getLevel() - Method in class woSource.math.VesselBranch

getLongestBranchPath() - Method in class woSource.math.VesselTree

9/2/2012 intent is to find the longest branch path, starting from the farthest branch and tracing backwards via parents.

getLoopedLocIndexForFromBr(int, int) - Method in class woSource.VesselSegm

uses int[][] loopLocs[nLoopPts][4] = [looped-to br, looped-to tree, looped-from br, looped-from tree].

getLoopedLocIndexForToBr(int, int) - Method in class woSource.VesselSegm

uses int[][] loopLocs[nLoopPts][4] = [looped-to br, looped-to tree, looped-from br, looped-from tree].

getLungMask(boolean) - Method in class woSource.humanLungSegm

getLungMask() - Method in class woSource.LIDCreview

getLungMask(boolean) - Method in class woSource.noduleDetection

GetLungVolRect_Mask(short[][][], String) - Method in class woSource.DoseVsIntensity

getMagnification() - Method in class woSource.math.ArrayDisplay

getMask() - Method in class woSource.lungSnake

getMask(int, int) - Method in class woSource.math.Polygon2D

getMaskImage() - Method in class woSource.math.SeriesImagesClass

getMax() - Method in class woSource.InteractiveSnake.Candidates

getMaxPt() - Method in class woSource.InteractiveSnake.Candidates

getMediastinumMask(boolean[][][]) - Static method in class woSource.math.ImgProc

getMiddlePoint() - Method in class woSource.math.VesselBranch

getMidSeptumTheta() - Method in class woSource.math.HeartLongAxis

getMIPslice(short[][][], float, float, float, float) - Static method in class woSource.math.ImgProc

get projection data at one projection slice, given by theta (rot about original Yaxis=vertical) and phi (rot about original Xaxis=horizontal)

getMIPslice(short[][][], float, float, float, float, boolean) - Static method in class woSource.math.ImgProc

getMIPslice(short[][][], float, float, float, float, int, int, boolean, int, int, boolean) - Static method in class woSource.math.ImgProc

getMIPslice(short[][][], float, float, float, float, int, int, int, float, int, int, boolean, int, int, boolean) - Static method in class woSource.math.ImgProc

getMIPslice(byte[][][], float, float, float, float) - Static method in class woSource.math.ImgProc

rotation around the original coordinate system.

getMIPslice(byte[][][], float, float, float, float, int, int) - Static method in class woSource.math.ImgProc

getMIPslice(byte[][][], float, float, float, float, boolean) - Static method in class woSource.math.ImgProc

getMIPslice(byte[][][], float, float, float, float, int, int, boolean, int, int, boolean) - Static method in class woSource.math.ImgProc

getMIPslice(byte[][][], float, float, float, float, int, int, int, float, int, int, boolean, int, int, boolean) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(short[][][], ImgProc.MIPcalcStruc, float, float, float) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(short[][][], ImgProc.MIPcalcStruc, float, float, float, boolean) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(short[][][], ImgProc.MIPcalcStruc, float, float, float, int, int, boolean, boolean, int, int) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(short[][][], ImgProc.MIPcalcStruc, float, int, int, int, float, int, int, boolean, boolean, int, int) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(short[][][], float, float, float) - Static method in class woSource.math.ImgProc

Uses global miprot[][] to keep track of previous rotations.

getMIPsliceIncr(short[][][], float, float, float, boolean) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(short[][][], float, float, float, int, int, boolean, boolean, int, int) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(short[][][], float, float, float, int, int, int, float, int, int, boolean, boolean, int, int) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(byte[][][], float, float, float) - Static method in class woSource.math.ImgProc

WO 8/13/2012 add feature to scale output pixel intensity by z value -- to give depth appearance to boolean data (of skeletonized vessels) Uses global miprot[][] to keep track of previous rotations.

getMIPsliceIncr(byte[][][], float, float, float, boolean) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(byte[][][], float, float, float, int, int, boolean) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(byte[][][], float, float, float, int, int, boolean, boolean, int, int) - Static method in class woSource.math.ImgProc

getMIPsliceIncr(byte[][][], float, float, float, int, int, int, float, int, int, boolean, boolean, int, int) - Static method in class woSource.math.ImgProc

getMIPsliceIncrLabeled(byte[][][], float, float, float, byte[][][]) - Static method in class woSource.math.ImgProc

WO 8/13/2012 add feature to scale output pixel intensity by z value -- to give depth appearance to boolean data (of skeletonized vessels)

getMIPsliceIncrLabeled(byte[][][], float, float, float, boolean, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceIncrLabeled(byte[][][], float, float, float, int, int, boolean, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceIncrLabeled(byte[][][], float, float, float, int, int, boolean, boolean, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceIncrLabeled(byte[][][], float, float, float, int, int, boolean, boolean, byte[][][], int, int) - Static method in class woSource.math.ImgProc

getMIPsliceIncrLabeled(byte[][][], float, float, float, int, int, int, float, int, int, boolean, boolean, byte[][][], int, int) - Static method in class woSource.math.ImgProc

getMIPsliceIncrLabeled(short[][][], float, float, float, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceIncrLabeled(short[][][], float, float, float, boolean, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceIncrLabeled(short[][][], float, float, float, int, int, boolean, boolean, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceIncrLabeled(short[][][], float, float, float, int, int, boolean, boolean, byte[][][], int, int) - Static method in class woSource.math.ImgProc

getMIPsliceIncrLabeled(short[][][], float, float, float, int, int, int, float, int, int, boolean, boolean, byte[][][], int, int) - Static method in class woSource.math.ImgProc

getMIPsliceLabeled(byte[][][], float, float, float, byte[][][]) - Static method in class woSource.math.ImgProc

WO 12/18/2012 want to return an image that can be colorized.

getMIPsliceLabeled(byte[][][], float, float, float, int, int, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceLabeled(byte[][][], float, float, float, int, int, boolean, boolean, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceLabeled(byte[][][], float, float, float, int, int, boolean, boolean, byte[][][], int) - Static method in class woSource.math.ImgProc

getMIPsliceLabeled(byte[][][], float, float, float, int, int, int, float, int, int, boolean, boolean, byte[][][], int) - Static method in class woSource.math.ImgProc

getMIPsliceLabeled(short[][][], float, float, float, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceLabeled(short[][][], float, float, float, int, int, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceLabeled(short[][][], float, float, float, int, int, boolean, boolean, byte[][][]) - Static method in class woSource.math.ImgProc

getMIPsliceLabeled(short[][][], float, float, float, int, int, boolean, boolean, byte[][][], int) - Static method in class woSource.math.ImgProc

getMIPsliceLabeled(short[][][], float, float, float, int, int, int, float, int, int, boolean, boolean, byte[][][], int) - Static method in class woSource.math.ImgProc

getmmPerPixelX() - Method in class woSource.math.ArrayDisplay

getmmPerPixelY() - Method in class woSource.math.ArrayDisplay

getMostRecentBranch() - Method in class woSource.math.VesselTree

getMostRecentIndex() - Method in class woSource.math.VesselTree

getNbPoints() - Method in class woSource.InteractiveSnake.Snake

getNbranches() - Method in class woSource.math.VesselTree

getNbranchesAtLevel(int) - Method in class woSource.math.VesselTree

getNcatchFileInfo() - Method in class woSource.DicomAnon

getNendSkipPts(float) - Method in class woSource.math.VesselBranch

getNextButton() - Method in class woSource.GenericRecallableDialog

Returns the contents of the next buttons_touched field.

getNfrontSkipPts(float) - Method in class woSource.math.VesselBranch

getNlevels() - Method in class woSource.math.VesselTree

getNodeSimImage(int, Rectangle3D, VesselBranch) - Method in class woSource.math.VesselBranch

getNodeSimImage(int, Rectangle3D, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

getNodeSimImage(int, float, Rectangle3D, VesselBranch) - Method in class woSource.math.VesselBranch

getNodeSimImage(int, float, float, Rectangle3D, VesselBranch, boolean) - Method in class woSource.math.VesselBranch

getNormalThroughEdgePt(boolean[][][], Point3Dint, int) - Static method in class woSource.math.ImgProc

getNormalThroughEdgePt(boolean[][][], int, int, int, int) - Static method in class woSource.math.ImgProc

getObjectBoundingBox(byte[][][], int, int, int) - Static method in class woSource.math.ImgProc

WO 12/22/10 get bounding box for the object connected to pointinside within the thresholded (binary) image

getObjectBoundingBox(byte[][][], int, int, int, int) - Static method in class woSource.math.ImgProc

getObjectContour(byte[][][], int, int, int) - Static method in class woSource.math.ImgProc

WO 2/14/11 assume that the image is basically a mask such that the pixel value at the seed demarks the object from the surroundings and the value will be either 0, 255 or 128

getObjectMask() - Method in class woSource.LIDCreview

getObjectMaskFromFiles() - Method in class woSource.ImageReviewer

getObjectMaskFromFiles(String) - Method in class woSource.ImageReviewer

getOrphanedBranchOfTopPt(int[]) - Method in class woSource.VesselSegm

getOuterContour(boolean[][]) - Static method in class woSource.math.ImgProc

routines to automatically detect outer surface contour
Short assumes the image center is inside ROI and walks out from center
Byte works with roi, if none found uses bounding box.

getOuterContour(boolean[][], Rectangle) - Static method in class woSource.math.ImgProc

getOuterContour(byte[][]) - Static method in class woSource.math.ImgProc

getOuterContour(byte[][], Rectangle) - Static method in class woSource.math.ImgProc

getOuterContour(boolean[][][]) - Static method in class woSource.math.ImgProc

getOuterContour(boolean[][][], Rectangle) - Static method in class woSource.math.ImgProc

getOuterContour(byte[][][]) - Static method in class woSource.math.ImgProc

getOuterContour(byte[][][], Rectangle) - Static method in class woSource.math.ImgProc

getOuterContour(byte[][][], Rectangle3D) - Static method in class woSource.math.ImgProc

WO 2/14/11 true 3D version

getOuterContour(short[][]) - Static method in class woSource.math.ImgProc

Short versions use Roi vs and 100 projection angles

getOuterContour(short[][], int) - Static method in class woSource.math.ImgProc

getOuterContour(short[][], int, int) - Static method in class woSource.math.ImgProc

getOuterContour(short[][], int, int, Roi) - Static method in class woSource.math.ImgProc

getOuterContour(short[][][]) - Static method in class woSource.math.ImgProc

getOuterContour(short[][][], int) - Static method in class woSource.math.ImgProc

getOuterContour(short[][][], int, int) - Static method in class woSource.math.ImgProc

getOuterContour(short[][][], int, int, Roi) - Static method in class woSource.math.ImgProc

getOutput() - Method in class woSource.math.ImgProc.CorrCalcThread

getOutput() - Method in class woSource.math.ImgProc.DilateThread

getOutput() - Method in class woSource.math.ImgProc.EdgeFillThread

getOutput() - Method in class woSource.math.ImgProc.ErodeThread

getOutputBoolean() - Method in class woSource.math.ImgProc.EdgeFillThread

getOutputByte() - Method in class woSource.math.ImgProc.ConvolveThread

getOutputFloat() - Method in class woSource.math.ImgProc.ConvolveThread

getOutputInt() - Method in class woSource.math.ImgProc.ConvolveThread

getOutputShort() - Method in class woSource.math.ImgProc.ConvolveThread

getPadding(float) - Method in class woSource.noduleDetectionModule

getPairNCCC(int, int, int, int) - Method in class woSource.VesselSegm

getPairTrimmedNCCC(int, int, int, int) - Method in class woSource.VesselSegm

getParentIndex() - Method in class woSource.math.VesselBranch

getPixel3Dcoords(int, int, int, Rectangle3D, Properties[]) - Static method in class woSource.math.ImgProc

get 3D mm coords for pixel.

getPixels() - Method in class woSource.math.ArrayDisplay

getPixels(boolean[][][]) - Method in class woSource.math.ArrayDisplay

getPixels(boolean[][]) - Method in class woSource.math.ArrayDisplay

getPixels(boolean[][], int) - Method in class woSource.math.ArrayDisplay

getPixels(float[][]) - Method in class woSource.math.ArrayDisplay

getPixels(float[][][]) - Method in class woSource.math.ArrayDisplay

getPixels(short[][][]) - Method in class woSource.math.ArrayDisplay

getPixels(int[][][]) - Method in class woSource.math.ArrayDisplay

getPixels(byte[][][]) - Method in class woSource.math.ArrayDisplay

getPixels(byte[][]) - Method in class woSource.math.ArrayDisplay

getPixels(byte[][], int) - Method in class woSource.math.ArrayDisplay

getPixels(short[][]) - Method in class woSource.math.ArrayDisplay

getPixels(short[][], int) - Method in class woSource.math.ArrayDisplay

getPixelToScannerCoords(int, int, int, boolean[][][]) - Method in class woSource.math.Image3Dinfo

getPixelValue(int, int) - Method in class woSource.math.SimTagImageInfo

getPoint(int) - Method in class woSource.math.VesselBranch

getPoints() - Method in class woSource.InteractiveSnake.SnakeStack

getPolygon2D() - Method in class woSource.InteractiveSnake.SnakeStack

getProperties() - Method in class woSource.math.ArrayDisplay

getProperty(String) - Method in class woSource.math.ArrayDisplay

getPScoeffs() - Method in class woSource.ImageRegistrationPS

getPSfitOrder() - Method in class woSource.ImageRegistrationPS

getPtInputDirInfo(String) - Method in class woSource.ImageReviewer

getPtSep(int, int) - Method in class woSource.math.VesselBranch

getPtSep(int, Point3Dint) - Method in class woSource.math.VesselBranch

getRadiusHistogram(int) - Method in class woSource.math.VesselTree

getRadiusHistogram(int) - Method in class woSource.VesselSegm

getRankingIndex(int[][], int[], int, int, int) - Static method in class woSource.math.ArraysI

WO 5/18/2012 find where the current 'val' belongs in the unsorted list A[list index][4=x,y,z,value] but with sorting accomplished by int[] rankIndices which ranks low to high.

getReal() - Method in class woSource.math.Complex

getRGBs(byte[][], byte[][], byte[][]) - Method in class woSource.math.ArrayColorDisplay

getRGBs(byte[][][], byte[][][], byte[][][]) - Method in class woSource.math.ArrayColorDisplay

getRoi(TruncatedEllipseRoi) - Method in class woSource.InteractiveSnake.Snake

getRoi(OvalRoi) - Method in class woSource.InteractiveSnake.Snake

getRoi() - Method in class woSource.InteractiveSnake.Snake

getRoi() - Method in class woSource.math.ArrayDisplay

getRoi(PolygonRoi) - Method in class woSource.math.ArrayDisplay

getRoi(EllipseRoi) - Method in class woSource.math.ArrayDisplay

getRoi(TruncatedEllipseRoi) - Method in class woSource.math.ArrayDisplay

getRoi(OvalRoi) - Method in class woSource.math.ArrayDisplay

getRoi() - Method in class woSource.math.Rectangle3D

getRoi() - Method in class woSource.MIPSviewer

getRoi() - Method in class woSource.MIPSviewerColor

getRoi() - Method in class woSource.Point3Dviewer

getROI3Dcoords(short[][][], Rectangle3D, Properties[]) - Static method in class woSource.math.ImgProc

get 3D mm coords and pixel value of each pixel within the ROI rectangle.

getRoiRect() - Method in class woSource.InteractiveSnake.Snake

getRoiRect() - Method in class woSource.InteractiveSnake.SnakeStack

getRoiVoxelToScannerCoords(boolean[][][]) - Method in class woSource.math.Image3Dinfo

getRotMtx(int) - Static method in class woSource.math.ArraysI

WO 6/29/04 int version for angles in degrees

getRotMtx(float) - Static method in class woSource.math.ArraysI

float version, already in radians

getRotMtx(int, int, int) - Static method in class woSource.math.ArraysI

getRotMtx(float, float, float) - Static method in class woSource.math.ArraysI

this should work for any right handed coordinate system, where A is the first rotation about the first (X usually) axis, B is the rotation about the second (usu.

getScreenLocation() - Method in class woSource.math.ArrayDisplay

WO 2/2/11 gets top-left corner location of frame on screen, not of mouse coords in window usage: Point.x, .y

getScreenSize() - Method in class woSource.math.ArrayDisplay

gets size of the window for this display (not the size of the computer monitor) usage: Dimension.width, .height

getSepAngle(int, int, boolean, int, int, boolean) - Method in class woSource.VesselSegm

goal to compute the trajectory angle in degrees between the two branch ends, skipping the first few points because their trajectory can be altered by the presence of the bifurcation or crossing.

getSepAngle(VesselBranch, boolean, VesselBranch, boolean) - Method in class woSource.VesselSegm

getSiblingBifurAngle(int, int) - Method in class woSource.VesselSegm

getSiblingFrontVec(int, int) - Method in class woSource.VesselSegm

getSideViewScreenSize() - Method in class woSource.math.ArrayColorDisplay3D

getSimImage(int, int, int) - Method in class woSource.math.VesselTree

Compute the simImg if it doesn't exist already.

getSimImage(int, int, int, Rectangle3D) - Method in class woSource.math.VesselTree

getSimImage() - Method in class woSource.VesselSegm

getSimImage(int) - Method in class woSource.VesselSegm

getSlice(short[][][], int) - Static method in class woSource.math.ArraysI

getSliceCenterSep() - Method in class woSource.math.ArrayDisplay

getSliceLabel(int) - Method in class woSource.math.ArrayDisplay

getSliceLabels() - Method in class woSource.math.ArrayDisplay

getSliceZ(int) - Method in class woSource.math.ArrayDisplay

getSmoothedPolygon(Polygon2D) - Static method in class woSource.math.MathII

getSmoothedPolygon(float[][]) - Static method in class woSource.math.MathII

getSmoothPolygon2D() - Method in class woSource.InteractiveSnake.SnakeStack

getSmoothPts(float[]) - Method in class woSource.math.VesselBranch

getSmoothPtsBoundingBox(float) - Method in class woSource.math.VesselBranch

getSmoothSnake3DPts(boolean) - Method in class woSource.InteractiveSnake.Snake

getSnake3DPts(boolean) - Method in class woSource.InteractiveSnake.Snake

getSortedIndices(float[], int) - Static method in class woSource.math.ArraysI

getStack3DSmoothPts() - Method in class woSource.InteractiveSnake.SnakeStack

getStackDepths(ImagePlus) - Method in class woSource.DoseVolumeStats

getStackDepths(ImagePlus) - Static method in class woSource.math.ImgProc

getStackSize() - Method in class woSource.math.ArrayDisplay

getStackWindow() - Method in class woSource.math.ArrayDisplay

getStringPoint3D(String, String) - Static method in class woSource.math.MathII

getStringPoint3D(String, String, int) - Static method in class woSource.math.MathII

getStringPoint3D(String, String, String) - Static method in class woSource.math.MathII

getStringPoint3D(String, String, int, String) - Static method in class woSource.math.MathII

getStringPoint3Dint(String, String, int, String) - Static method in class woSource.math.MathII

getStringString(String, String) - Static method in class woSource.math.MathII

parses string 'target' for String value following the tag 'key'

getStringString(String, String, int) - Static method in class woSource.math.MathII

getStringString(String, String, String) - Static method in class woSource.math.MathII

getStringString(String, String, int, String) - Static method in class woSource.math.MathII

getStringValue(String) - Static method in class woSource.math.MathII

getStringValue(String, String) - Static method in class woSource.math.MathII

getStringValue(String, String, int) - Static method in class woSource.math.MathII

getStringValue(String, String, String) - Static method in class woSource.math.MathII

getStringValue(String, String, int, String) - Static method in class woSource.math.MathII

parses the string for key (String) tag, and grabs first number following it.

getStringValues(String, String) - Static method in class woSource.math.MathII

getStringValues(String, int, String) - Static method in class woSource.math.MathII

getStringValues(String, int, String, int) - Static method in class woSource.math.MathII

getStringValues(String, int, String, String) - Static method in class woSource.math.MathII

getStringValues(String, int, String, int, String) - Static method in class woSource.math.MathII

getSurfMesh() - Method in class woSource.math.VesselBranch

getTagFilenameAddon(int, int) - Method in class woSource.HeartSegm

GetTagParams(short[][], int) - Method in class woSource.HeartSegm

GetTagParams(short[][], int, float, float, float) - Method in class woSource.HeartSegm

getTagValue(float, float) - Method in class woSource.math.SimTagImageInfo

getTangent(int) - Method in class woSource.math.VesselBranch

getTestImg() - Method in class woSource.math.Polygon2D

getTestTagImg(byte[][], float, float, float, float) - Method in class woSource.HeartSegm

getTopBranchIndex() - Method in class woSource.math.VesselTree

getTopLocIndex(Point3Dint) - Method in class woSource.VesselSegm

getTopViewScreenSize() - Method in class woSource.math.ArrayColorDisplay3D

getTortuosity() - Method in class woSource.math.VesselBranch

getTortuosityHistogram(int) - Method in class woSource.math.VesselTree

getTransformedImageCoords_mm(short[][][], Properties[], Rectangle3D, ImageRegistration, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

get 3D mm transformed coords and pixel value of each pixel within the ROI rectangle, using the same code as above.

getTransformedImageCoords_mm(short[][][], Properties[], Rectangle3D, float, float, float, float, float, float, float, float, float, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

getTransformedPtCoords_mm(int, int, int) - Method in class woSource.ImageRegistration

transform the voxel dwh into the deformed coord system and return the mm scanner coords in xyz order.

getTransformedPtCoords_mm(float, float, float) - Method in class woSource.ImageRegistration

getTransformedPtCoords_mm(int, int, int) - Method in class woSource.ImgRegistration

transform the voxel dwh into the deformed coord system and return the mm coords in xyz order.

getTransformedPtCoords_mm(float, float, float) - Method in class woSource.ImgRegistration

getTransformedPtCoords_mm(int, int, int, Properties[], Rectangle3D, ImageRegistration, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

Intent is to pass in the image pixel coords d,w,h and transform them according to the existing registration parameters to get the tranformed 3D point coords in mm in scanner coords of the target set.

getTransformedPtCoords_mm(int, int, int, Properties[], Rectangle3D, float, float, float, float, float, float, float, float, float, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

getTransformedPtCoords_mm(float, float, float, Properties[], Rectangle3D, ImageRegistration, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

getTransformedPtCoords_mm(float, float, float, Properties[], Rectangle3D, float, float, float, float, float, float, float, float, float, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

getTransformedPtCoords_px(int, int, int) - Method in class woSource.ImageRegistration

transform the voxel dwh into the deformed coord system and return the sub-voxel coords dwh.

getTransformedPtCoords_px(float, float, float) - Method in class woSource.ImageRegistration

getTransformedPtCoords_px(int, int, int) - Method in class woSource.ImgRegistration

transform the voxel dwh into the deformed coord system and return the sub-voxel coords dwh.

getTransformedPtCoords_px(float, float, float) - Method in class woSource.ImgRegistration

getTransformedPtCoords_px(int, int, int, Properties[], Rectangle3D, ImageRegistration, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

Intent is to pass in the image pixel coords d,w,h and transform them according to the existing registration parameters to get the tranformed 3D pixel coords in (dwh) with sub-pixel precision in the scanner coords of the target set.

getTransformedPtCoords_px(int, int, int, Properties[], Rectangle3D, float, float, float, float, float, float, float, float, float, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

getTransformedPtCoords_px(float, float, float, Properties[], Rectangle3D, ImageRegistration, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

getTransformedPtCoords_px(float, float, float, Properties[], Rectangle3D, float, float, float, float, float, float, float, float, float, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

getTreeBranchLabels() - Method in class woSource.VesselSegm

getTreeMask() - Method in class woSource.math.VesselTree

getTreeTop() - Method in class woSource.math.VesselTree

getTreeTopPt3D() - Method in class woSource.math.VesselTree

getTrimmedBranchEndVec(int, int) - Method in class woSource.VesselSegm

getTrimmedBranchFrontVec(int, int) - Method in class woSource.VesselSegm

getTrimmedBranchLength(int, int) - Method in class woSource.VesselSegm

getTrimmedBranchRadius(int, int) - Method in class woSource.VesselSegm

getTrimmedBranchRadius(int, int, float, float) - Method in class woSource.VesselSegm

getValues() - Method in class woSource.Deconvolver

getVolume() - Method in class woSource.math.VesselBranch

getVolume() - Method in class woSource.math.VesselTree

compute vascular volume as sum_brs{br_len*br_area)

getVoxelToScannerCoords(int, int, int, boolean[][][]) - Method in class woSource.math.Image3Dinfo

getVoxelVisits() - Method in class woSource.CellMigration

getWHDdirs(String) - Static method in class woSource.math.ImgProc

getWidth() - Method in class woSource.math.ArrayDisplay

getWriteTreeSimImage(VesselTree) - Method in class woSource.PulmonaryTrunkSegm

getWriteTreeSTL(VesselTree) - Method in class woSource.PulmonaryTrunkSegm

getWrot() - Method in class woSource.ImageRegistration

getWrot() - Method in class woSource.ImgRegistration

getWscale() - Method in class woSource.ImageRegistration

getWscale() - Method in class woSource.ImgRegistration

getXshift() - Method in class woSource.ImageRegistration

getXshift() - Method in class woSource.ImgRegistration

getYshift() - Method in class woSource.ImageRegistration

getYshift() - Method in class woSource.ImgRegistration

getZshift() - Method in class woSource.ImageRegistration

getZshift() - Method in class woSource.ImgRegistration

giveDoneButFocus() - Method in class woSource.GenericRecallableDialog

go(ArrayDisplay) - Method in class woSource.lungSnake

go(ArrayDisplay, ArrayDisplay) - Method in class woSource.lungSnake

go() - Method in class woSource.noduleDetection.lungSnake

goodread - Variable in class woSource.InteractiveSnake.Snake

goodReadOrAdjusted() - Method in class woSource.InteractiveSnake.SnakeStack

gradient(byte[][], Rectangle) - Static method in class woSource.math.ArraysI

gradient(byte[][]) - Static method in class woSource.math.ArraysI

gradient(byte[][][]) - Static method in class woSource.math.ArraysI

gradient(byte[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

gradient(short[][]) - Static method in class woSource.math.ArraysI

gradient(short[][], Rectangle) - Static method in class woSource.math.ArraysI

gradient(short[][][]) - Static method in class woSource.math.ArraysI

gradient(short[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

gradient(float[][]) - Static method in class woSource.math.ArraysI

gradient(float[][], Rectangle) - Static method in class woSource.math.ArraysI

gradient2D(byte[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

gradient2D(byte[][][]) - Static method in class woSource.math.ArraysI

gradient2D(short[][][]) - Static method in class woSource.math.ArraysI

gradient2D(short[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

GradientAnalysis3D - Class in woSource

GradientAnalysis3D() - Constructor for class woSource.GradientAnalysis3D

gradientIn - Static variable in class woSource.InteractiveSnake

gradientIn(byte[][], Rectangle) - Static method in class woSource.math.ArraysI

gradientIn(short[][], Rectangle) - Static method in class woSource.math.ArraysI

gradientMag(boolean[][]) - Static method in class woSource.math.ArraysI

WO 3/19/03 added roi feature
3/23/03 for 'binary' images, do not want to smear out edge over two pixels, rather put it on the high pixel.

gradientMag(boolean[][], Rectangle) - Static method in class woSource.math.ArraysI

WO 6/13/05 duh, this works for binary images, not byte images.

gradientMag(boolean[][][]) - Static method in class woSource.math.ArraysI

gradientMag(boolean[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

gradientMag(byte[][]) - Static method in class woSource.math.ArraysI

WO 6/5/2013 created accurate grad calc for byte (used to be the boolean version above).

gradientMag(byte[][], Rectangle) - Static method in class woSource.math.ArraysI

gradientMag(byte[][][]) - Static method in class woSource.math.ArraysI

gradientMag(byte[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

gradientMag2D(boolean[][][]) - Static method in class woSource.math.ArraysI

gradientMag2D(boolean[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

gradientMag2D(byte[][][]) - Static method in class woSource.math.ArraysI

gradientMag2D(byte[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

gradientOut - Static variable in class woSource.InteractiveSnake

gradientOut(byte[][], Rectangle) - Static method in class woSource.math.ArraysI

gradientOut(short[][], Rectangle) - Static method in class woSource.math.ArraysI

gradientType - Variable in class woSource.InteractiveSnake

gradKernel(float[][], int) - Static method in class woSource.math.MathII

WO 11/13/00 generic-sized profile gradient kernel
define via 2D image gradient operator on original kernel
designed as (n+2)x(n+2) for an n sized primary template
want value of background intensity of original template to use for grad calc at edges.

greatestArea() - Method in class woSource.math.Polygon3D

greatestDiameter() - Method in class woSource.math.Polygon2D

greatestDiameter() - Method in class woSource.math.Polygon3D

H

H - Static variable in class woSource.ImageRegistration

handleFailedBranchRepair(int, int) - Method in class woSource.VesselSegm

if got here then could not find any matches.

HannWindow(int, float) - Static method in class woSource.math.MathII

Hann window, default: only filtering 10% edges
j== current index (==depth-at)
a== total depth
edge== is effective depth of windowing filter cutoff

HannWindow(int, float, float) - Static method in class woSource.math.MathII

HannWindow(float, float, float) - Static method in class woSource.math.MathII

hasChildren() - Method in class woSource.math.VesselBranch

hasFocus() - Method in class woSource.math.ArrayDisplay

WO 3/5/2015 corrected my earlier incorrect use of getFocusOwner()==null as it does not apply to windows or canvases, just components thereof.

hasFocus() - Method in class woSource.ScreenSelectorCanvas

hashCode() - Method in class woSource.math.Complex

hasMultipleLoopPairings(int, int) - Method in class woSource.VesselSegm

hasNoImage - Variable in class woSource.math.ArrayDisplay

hav() - Method in class woSource.math.Complex

hav(Complex) - Static method in class woSource.math.Complex

haveLungVolMaskImgs - Variable in class woSource.noduleDetectionModule

havePulmTrunkMask - Variable in class woSource.humanLungSegm

havePulmTrunkMask - Variable in class woSource.VesselSegm

HeartLongAxis - Class in woSource.math

HeartLongAxis(String) - Constructor for class woSource.math.HeartLongAxis

HeartLongAxis(String, Point3D, Point3D) - Constructor for class woSource.math.HeartLongAxis

HeartLongAxis(String, Point3D, Point3D, Point3D) - Constructor for class woSource.math.HeartLongAxis

HeartLongAxis(HeartLongAxis) - Constructor for class woSource.math.HeartLongAxis

HeartLongAxis(String, float, float, float, float, float, float) - Constructor for class woSource.math.HeartLongAxis

heartMR3Dinfo - Variable in class woSource.HeartSegm

heartRect - Variable in class woSource.math.SimTagImageInfo

HeartSegm - Class in woSource

2/2/2015 WO need place where I try to read in the existing tag points.

HeartSegm() - Constructor for class woSource.HeartSegm

heartSegmentor - Variable in class woSource.Point3Dviewer

Height - Variable in class woSource.DoseReader

Height - Variable in class woSource.DoseReader_Oct2012_oldUR

HEIGHT - Static variable in class woSource.math.ArrayDisplay

Height - Variable in class woSource.math.ArrayDisplay

height - Variable in class woSource.math.Rectangle3D

height - Variable in class woSource.math.SeriesImagesClass

Hermite_00(float) - Static method in class woSource.math.MathII

Cubic Hermite interpolation functions The derivative needs to be in units of distance, thus multiply the dimension-less slope value by elem_len prior to sending to here.

Hermite_00(double) - Static method in class woSource.math.MathII

Hermite_01(float) - Static method in class woSource.math.MathII

Hermite_01(double) - Static method in class woSource.math.MathII

Hermite_10(float) - Static method in class woSource.math.MathII

Hermite_10(double) - Static method in class woSource.math.MathII

Hermite_11(float) - Static method in class woSource.math.MathII

Hermite_11(double) - Static method in class woSource.math.MathII

hide() - Method in class woSource.math.ArrayDisplay

hide() - Method in class woSource.Point3Dviewer

hideAllDisplays() - Method in class woSource.PulmonaryTrunkSegm

hideDialog() - Method in class woSource.GenericRecallableDialog

hideGUI() - Method in class woSource.MIPSviewer

highlightButton(int) - Method in class woSource.GenericRecallableDialog

HistoBinAdjuster - Class in woSource

HistoBinAdjuster() - Constructor for class woSource.HistoBinAdjuster

HistoHisto_reg - Class in woSource

HistoHisto_reg() - Constructor for class woSource.HistoHisto_reg

HistoMR_registration - Class in woSource

HistoMR_registration(short[][][], Properties[], Rectangle3D, short[][][], Properties[], Rectangle3D, ArrayColorDisplay3D) - Constructor for class woSource.HistoMR_registration

HistoMRreg - Class in woSource

HistoMRreg() - Constructor for class woSource.HistoMRreg

HistoSlideLighting - Class in woSource

HistoSlideLighting() - Constructor for class woSource.HistoSlideLighting

humanLungSegm - Class in woSource

humanLungSegm() - Constructor for class woSource.humanLungSegm

HyperSkelPair - Class in woSource.math

for vesselSegmentation, when a tree crosses another you need a hyperskel pair to jump the crossing

HyperSkelPair() - Constructor for class woSource.math.HyperSkelPair

HyperSkelPair(HyperSkelPair) - Constructor for class woSource.math.HyperSkelPair

hypot(Complex, Complex) - Static method in class woSource.math.Complex

I

ID_OFFSET - Static variable in class woSource.DicomAnon

identity(float[][]) - Static method in class woSource.math.ArraysI

returns identity matrix of same dims as A

identity(int, int) - Static method in class woSource.math.ArraysI

return identity matrix of dims WxH

identity(float[][][]) - Static method in class woSource.math.ArraysI

returns identity matrix of same dims as A

Image3Dinfo - Class in woSource.math

Image3Dinfo() - Constructor for class woSource.math.Image3Dinfo

Image3Dinfo(String, int, Rectangle3D, float[][], float[], float[], float[], float, float, int[], float[][], String[][]) - Constructor for class woSource.math.Image3Dinfo

Image3Dinfo(Image3Dinfo) - Constructor for class woSource.math.Image3Dinfo

ImageGradientOverlay(short[][][]) - Method in class woSource.math.ArrayColorDisplay

ImageGradientOverlay(short[][][], int, int, int) - Method in class woSource.math.ArrayColorDisplay

imagemax - Variable in class woSource.PulmonaryTrunkSegm

imagemax - Variable in class woSource.RatImageAdjuster

imagemax - Variable in class woSource.VesselSegm

imagemin - Variable in class woSource.PulmonaryTrunkSegm

imagemin - Variable in class woSource.RatImageAdjuster

imagemin - Variable in class woSource.VesselSegm

ImageOverlay - Class in woSource

ImageOverlay() - Constructor for class woSource.ImageOverlay

ImageOverlay(boolean[][]) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(byte[][]) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(byte[][], int, int) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(boolean[][][]) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(byte[][][]) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(byte[][][], int, int, int) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(byte[][][], int, int, int, String) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(short[][]) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(short[][], int, int) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(short[][][]) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(short[][][], String) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(short[][][], int, int, int) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(short[][][], int, int, int, String) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(short[][][], float, float, float, float, float, float, Rectangle3D) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(short[][][], float, float, float, float, float, float, Rectangle3D, String) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(float[][][]) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(float[][][], int, int, int) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(float[][][], int, int, int, String) - Method in class woSource.math.ArrayColorDisplay

ImageOverlay(short[][][], int, int, int) - Method in class woSource.math.ArrayColorDisplay3D

ImageOverlay(short[][][], Properties[], Rectangle3D, float, float, float, float, float, float) - Method in class woSource.math.ArrayColorDisplay3D

ImageOverlay(short[][][], Properties[], Rectangle3D, float, float, float, float, float, float, String) - Method in class woSource.math.ArrayColorDisplay3D

ImageOverlay(short[][][]) - Method in class woSource.math.ArrayColorDisplay3D

ImageOverlay(boolean[][], boolean[][]) - Method in class woSource.math.ArrayDisplay

WO 1/5/05 need to either pass in the original array values or store a back-up internally as you corrupt the displayed version each time an overlay is made.

ImageOverlay(boolean[][], boolean[][], int, int) - Method in class woSource.math.ArrayDisplay

ImageOverlay(byte[][], boolean[][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(boolean[][][], boolean[][][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(boolean[][][], boolean[][][], int, int, int) - Method in class woSource.math.ArrayDisplay

ImageOverlay(byte[][][], boolean[][][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(boolean[][][], byte[][][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(byte[][], byte[][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(byte[][], byte[][], int, int) - Method in class woSource.math.ArrayDisplay

ImageOverlay(byte[][][], byte[][][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(byte[][][], byte[][][], int, int, int) - Method in class woSource.math.ArrayDisplay

ImageOverlay(short[][], short[][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(short[][], short[][], int, int) - Method in class woSource.math.ArrayDisplay

ImageOverlay(short[][], boolean[][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(short[][][], boolean[][][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(boolean[][][], short[][][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(short[][][], short[][][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(short[][][], short[][][], int, int, int) - Method in class woSource.math.ArrayDisplay

ImageOverlay(float[][][], float[][][]) - Method in class woSource.math.ArrayDisplay

ImageOverlay(float[][][], float[][][], int, int, int) - Method in class woSource.math.ArrayDisplay

ImageRegistration - Class in woSource

ImageRegistration() - Constructor for class woSource.ImageRegistration

ImageRegistration(short[][], Properties, short[][], Properties) - Constructor for class woSource.ImageRegistration

ImageRegistration(short[][][], Properties[], short[][][], Properties[]) - Constructor for class woSource.ImageRegistration

ImageRegistration(short[][][], Properties[], Rectangle3D, short[][][], Properties[], Rectangle3D) - Constructor for class woSource.ImageRegistration

ImageRegistration(short[][][], Properties[], Rectangle3D, FileInfo, short[][][], Properties[], Rectangle3D, FileInfo) - Constructor for class woSource.ImageRegistration

ImageRegistrationPS - Class in woSource

ImageRegistrationPS() - Constructor for class woSource.ImageRegistrationPS

ImageRegistrationPS(ImageRegistrationPS) - Constructor for class woSource.ImageRegistrationPS

ImageRegistrationPS(int, SimTagImageInfo[], Image3Dinfo[], SeriesImagesClass[], HeartLongAxis) - Constructor for class woSource.ImageRegistrationPS

ImageReviewer - Class in woSource

ImageReviewer() - Constructor for class woSource.ImageReviewer

images - Variable in class woSource.math.SeriesImagesClass

imageStatsCorrelation(byte[][][], byte[][][]) - Static method in class woSource.math.ImgProc

WO 4/4/2013 want statistical correlation of 2 images evaluated only over the prescribed mask.

imageStatsCorrelation(byte[][][], byte[][][], Rectangle3D) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(byte[][][], byte[][][], boolean[][][]) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(byte[][][], byte[][][], boolean[][][], Rectangle3D) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][][], byte[][][]) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][][], byte[][][], boolean[][][]) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][][], byte[][][], Rectangle3D) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][][], byte[][][], boolean[][][], Rectangle3D) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][], byte[][], boolean[][]) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(byte[][], byte[][], boolean[][]) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][], short[][], boolean[][]) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][], byte[][]) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][][], short[][][]) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][][], short[][][], boolean[][][]) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][][], short[][][], Rectangle3D) - Static method in class woSource.math.ImgProc

imageStatsCorrelation(short[][][], short[][][], boolean[][][], Rectangle3D) - Static method in class woSource.math.ImgProc

imagesWereSaved - Variable in class woSource.RatImageAdjuster

ImageXdir - Variable in class woSource.math.Image3Dinfo

ImageYdir - Variable in class woSource.math.Image3Dinfo

ImageZdir - Variable in class woSource.math.Image3Dinfo

imgHeight - Variable in class woSource.math.SimTagImageInfo

imgHeight - Variable in class woSource.Point3Dviewer

imgMask - Variable in class woSource.math.VesselBranch

ImgProc - Class in woSource.math

miscellaneous image processing routines

ImgProc() - Constructor for class woSource.math.ImgProc

ImgProc.ConvolveThread - Class in woSource.math

note that this class is defined to run static function convolve.

ImgProc.CorrCalcThread - Class in woSource.math

this class is to run the static function statsCorrCirc

ImgProc.DilateThread - Class in woSource.math

note that this class is defined to run static function erode
WO 10/3/2012 This works by defining a unique Roi for each thread to work on.

ImgProc.EdgeFillThread - Class in woSource.math

note that this class is defined to run static function edgeFill

ImgProc.ErodeThread - Class in woSource.math

This class is defined to run static function erode
WO 10/3/2012 This works by defining a unique Roi for each thread to work on.

ImgProc.MIPcalcStruc - Class in woSource.math

public static byte[][][] distTransform (boolean[][][] origBinImg ) { return distTransform(ArraysI.toByte(origBinImg)); } // 3D distance transform public static byte[][][] distTransform( byte[][][] origBinImg ) { int depth = origBinImg.length; int width = origBinImg[0].length; int height = origBinImg[0][0].length; byte[][][] distmap = new byte[depth][width][height]; ArraysI.copy(origBinImg, distmap); //WO for now invert the image ArraysI.scale(distmap, 255,0); // final int a = 3, b = 4, c = 3, d = 4, e = 5; //alternate weights final int a = 3, b = 4, c = 5, d = 3, e = 7; final int[] wf = new int[] { e, d, e, d, c, d, e, d, e, b, a, b, a, 255, 255, 255, 255, 255, }; final int[] wb = new int[] { 255, 255, 255, 255, 255, a, b, a, b, e, d, e, d, c, d, e, d, e, }; int[] slask = new int[2 * 3 * 3]; // Border pixels are ignored to simplify the convolutions below for (int z = 0; z < depth; z++) for (int x = 0; x < width; x++) for (int y = 0; y < height; y++) if (z == 0 || x == 0 || y == 0 || z == depth - 1 || y == height - 1 || x == width - 1) distmap[z][x][y] = (byte) 0x0; // Forward iteration for (int z = 1; z < depth-1; z++) { IJ.showProgress(z, 2 * depth - 2); for (int x = 1; x < width-1; x++) { for (int y = 1; y < height-1; y++) { for (int k = -1; k < 1; k++) for (int j = -1; j < 2; j++) for (int i = -1; i < 2; i++) { int slaskindex = (i+1)+ (j+1)*3 + (k+1)*3*3; int pixel = distmap[z+k+1][x+i][y+j]&0xff; // 0xff & ((byte[]) imRef.getStack().getPixels(z+k+1))[(x+i)+ (y+j)* width]; slask[slaskindex] = pixel + wf[slaskindex]; } int minval = slask[0]; // the lowest value so far for (int i = 1; i < slask.length; i++) if ((slask[i]) < minval) minval = (slask[i]); // int pixel = 0xff & ((byte[]) imRef.getStack().getPixels(z+1))[(x)+ (y)* width]; int pixel = distmap[z+1][x][y]&0xff; if (pixel > minval) // ((byte[]) imRef.getStack().getPixels(z+1))[x + y*width] = (byte) (minval & 0xff); distmap[z+1][x][y] = (byte) (minval); } // end height(y) } // end width(x) } // end depth(z) // Backward iteration for (int z = depth-3; z > 0; z--) { // WO 3/08 changed from depth-2 to depth-3 IJ.showProgress(2 * depth - z, 2 * depth - 2); for (int x = width-2; x > 0; x--) { for (int y = height-2; y > 0; y--) { for (int k = 0; k < 2; k++) for (int j = -1; j < 2; j++) for (int i = -1; i < 2; i++) { int slaskindex = (i+1)+ (j+1)*3+ (k)*3*3; int pixel = distmap[z+k+1][x+i][y+j]&0xff; // = 0xff & ((byte[]) imRef.getStack().getPixels(z+k+1))[(x+i)+ (y+j)*width]; slask[slaskindex] = pixel + wb[slaskindex]; } int minval = slask[0]; // the lowest value so far for (int i = 1; i < slask.length; i++) if ((slask[i]) < minval) minval = (slask[i]); int pixel = distmap[z+1][x][y]&0xff; // = 0xff & ((byte[]) imRef.getStack().getPixels(z+1))[(x)+ (y)*width]; if (pixel > minval) // ((byte[]) imRef.getStack().getPixels(z+1))[x + y*width] = (byte) (minval &0xff); distmap[z+1][x][y] = (byte) (minval); } // end height(y) } // end width(x) } // end depth(z) return distmap; } // 3D distance transform

ImgRegistration - Class in woSource

This is a front end to ImageRegistration(), where the latter has the GUI.

ImgRegistration() - Constructor for class woSource.ImgRegistration

imgWidth - Variable in class woSource.math.SimTagImageInfo

imgWidth - Variable in class woSource.Point3Dviewer

imp - Variable in class woSource.WindowLevelAdjuster

imreg - Variable in class woSource.HeartSegm

indentMask() - Method in class woSource.lungSnake

indentMask() - Method in class woSource.noduleDetection.lungSnake

infoToOutputString() - Method in class woSource.math.HeartLongAxis

init(ImagePlus) - Method in class woSource.HeartSegm

init(ImagePlus) - Method in class woSource.InteractiveSnake

snakestack == null is flag for interactiveSnake running as a stand-alone program

Init(Rectangle) - Method in class woSource.InteractiveSnake.Snake

Init(Roi) - Method in class woSource.InteractiveSnake.Snake

Init(InteractiveSnake.Snake) - Method in class woSource.InteractiveSnake.Snake

Init(Roi) - Method in class woSource.InteractiveSnake.SnakeStack

Init(Rectangle) - Method in class woSource.InteractiveSnake.SnakeStack

initBins(ImagePlus) - Method in class woSource.HistoBinAdjuster

initDicomRewriter(String, String, boolean) - Method in class woSource.DicomAnon

initialTraceAlongBranch(int, int, int, int, int) - Method in class woSource.VesselSegm

This traverses a tree (treeID) starting from skeletal/branch point loc x,y,z on branch (branchIndex).

initPtNodules() - Method in class woSource.LIDCreview

initSearch_ptSep - Variable in class woSource.lungSnake

initSnackStacks() - Method in class woSource.HeartSegm

InitSnakeDisplay(ArrayDisplay) - Method in class woSource.InteractiveSnake

similar to version from hermitsnake.

InitSnakeDisplay(String, ArrayDisplay) - Method in class woSource.InteractiveSnake

InitSnakeDisplay() - Method in class woSource.RegisterSnake

innerbodyROI - Variable in class woSource.humanLungSegm

inputdir - Variable in class woSource.humanLungSegm

InputParentDir - Static variable in class woSource.math.MathI

insert(int) - Method in class woSource.InteractiveSnake.Candidates

insert(Point2D) - Method in class woSource.InteractiveSnake.Candidates

insert(Point2D, int) - Method in class woSource.InteractiveSnake.Candidates

insert(int[], int, int) - Static method in class woSource.math.ArraysI

WO 5/23/2012 apparently by design this does not lengthen the array A, rather it just pushes the bottom value off the bottom of the array.

insert(int[], int, int, int) - Static method in class woSource.math.ArraysI

insert(int[][], int[], int) - Static method in class woSource.math.ArraysI

insert(int[][], int[], int, int) - Static method in class woSource.math.ArraysI

insert(float[], float, int) - Static method in class woSource.math.ArraysI

insert(Point2D[], Point2D, int) - Static method in class woSource.math.ArraysI

insert(Point3D[], Point3D, int) - Static method in class woSource.math.ArraysI

insert(Point3Dint[], Point3Dint, int) - Static method in class woSource.math.ArraysI

insert(NoduleCandidate[], NoduleCandidate, int) - Static method in class woSource.math.ArraysI

insert without extending array

insertDiskOntoMask(int, String) - Method in class woSource.math.VesselTree

12/24/2012 intent is to place a break int the mask to permit separation of mask into sub-tree masks.

insertDiskOntoMask(Point3Dint) - Method in class woSource.math.VesselTree

insertDiskOntoMask(int, int) - Method in class woSource.math.VesselTree

insertExtraPt(Point2D) - Method in class woSource.InteractiveSnake.Candidates

insertSubArray(boolean[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

WO 9/25/2013 insert subArray into bigger matrix space

insertSubArray(byte[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

insertSubArray(short[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

Int(float) - Static method in class woSource.math.MathI

Int(double) - Static method in class woSource.math.MathI

InteractiveSnake - Class in woSource

Inter-Active 'Snake' Segmentation by W.

InteractiveSnake() - Constructor for class woSource.InteractiveSnake

InteractiveSnake.Candidates - Class in woSource

InteractiveSnake.SmoothSnake - Class in woSource

InteractiveSnake.Snake - Class in woSource

InteractiveSnake.SnakeStack - Class in woSource

InteractiveSnake_Hermite - Class in woSource

InteractiveSnake_Hermite() - Constructor for class woSource.InteractiveSnake_Hermite

InteractiveSnake_Hermite(String) - Constructor for class woSource.InteractiveSnake_Hermite

InteractiveSnake_Hermite3D - Class in woSource

InteractiveSnake_Hermite3D() - Constructor for class woSource.InteractiveSnake_Hermite3D

InteractiveSnake_Hermite3D(String) - Constructor for class woSource.InteractiveSnake_Hermite3D

intestineErodDilRad - Variable in class woSource.humanLungSegm

inverse(Complex) - Static method in class woSource.math.Complex

inverse() - Method in class woSource.math.Complex

invert(boolean[][]) - Static method in class woSource.math.ArraysI

computes OFF/ON for each element != matrix inversion

invert(boolean[][][]) - Static method in class woSource.math.ArraysI

invertGrayscale(float[][]) - Static method in class woSource.math.ImgProc

invertGrayscale(float[][][]) - Static method in class woSource.math.ImgProc

invertGrayscale(short[][]) - Static method in class woSource.math.ImgProc

invertGrayscale(short[][][]) - Static method in class woSource.math.ImgProc

invertKernel(float[][]) - Static method in class woSource.math.MathII

assumes original kernel min==0

invertLUT() - Method in class woSource.math.ArrayDisplay

invTransDoseField() - Method in class woSource.DoseVsIntensity

want to warp the second image voxels and if the voxel center lands within the dose region, then find and record the closest dose sample.

invTransformPt_px(int, int, int, Properties[], Rectangle3D, ImageRegistration, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

Intent is to inverse-transform the voxel in the target image back to it's beginning voxel in the reference image using the existing affine image registration values, and using a cheap iterative approach.
WO 4/25/20913 This seems to be working correctly.

invTransformPt_px(float, float, float, Properties[], Rectangle3D, ImageRegistration, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

invTransformPt_px(int, int, int, Properties[], Rectangle3D, float, float, float, float, float, float, float, float, float, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

invTransformPt_px(float, float, float, Properties[], Rectangle3D, float, float, float, float, float, float, float, float, float, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

inwardBendAngle(Point2D, Point2D, Point2D) - Static method in class woSource.math.MathII

6/16/11 for my LIDC snake work

inwardConstraint - Variable in class woSource.InteractiveSnake.Snake

ips - Variable in class woSource.WindowLevelAdjuster

is45 - Variable in class woSource.math.SimTagImageInfo

isAhyperSkelPt(int, int, int) - Method in class woSource.VesselSegm

isAhyperSkelPt(Point3Dint) - Method in class woSource.VesselSegm

isALoopedFromLoc(int, int) - Method in class woSource.VesselSegm

isALoopedToLoc(int, int) - Method in class woSource.VesselSegm

isAtopLoc(Point3Dint) - Method in class woSource.VesselSegm

isByte - Variable in class woSource.math.ArrayDisplay

isByte(ImagePlus) - Static method in class woSource.math.ImgProc

isByte - Variable in class woSource.math.VesselTree

isColor(ImagePlus) - Static method in class woSource.math.ImgProc

isDicom(ImagePlus) - Static method in class woSource.math.ImgProc

isDouble - Variable in class woSource.math.ArrayDisplay

isEqual(Complex) - Method in class woSource.math.Complex

isEqual(Complex, Complex) - Static method in class woSource.math.Complex

isEqualWithinLimits(Complex, double) - Method in class woSource.math.Complex

isEqualWithinLimits(Complex, Complex, double) - Static method in class woSource.math.Complex

isEven(int) - Static method in class woSource.math.MathI

isFloat - Variable in class woSource.math.ArrayDisplay

isInfinite(Complex) - Static method in class woSource.math.Complex

isInfinite() - Method in class woSource.math.Complex

isInt - Variable in class woSource.math.ArrayDisplay

isLA - Variable in class woSource.HeartSegm

isMinusInfinity() - Method in class woSource.math.Complex

isMinusInfinity(Complex) - Static method in class woSource.math.Complex

isNaN(Complex) - Static method in class woSource.math.Complex

isNaN() - Method in class woSource.math.Complex

isOdd(int) - Static method in class woSource.math.MathI

isotropicSimTreeImg - Variable in class woSource.math.VesselTree

isPlusInfinity() - Method in class woSource.math.Complex

isPlusInfinity(Complex) - Static method in class woSource.math.Complex

isPoint3D - Variable in class woSource.math.ArrayDisplay

isPointInAnyTree(int, int, int) - Method in class woSource.VesselSegm

isPointInBranch(Point3Dint) - Method in class woSource.math.VesselBranch

isPointInTree(Point3Dint) - Method in class woSource.math.VesselTree

isReal(Complex) - Static method in class woSource.math.Complex

isReal(Complex[]) - Static method in class woSource.math.Complex

isReal() - Method in class woSource.math.Complex

isReal(Complex, double) - Static method in class woSource.math.Complex

isReal(Complex[], double) - Static method in class woSource.math.Complex

isReal(double) - Method in class woSource.math.Complex

isRealPerCent(Complex, double) - Static method in class woSource.math.Complex

isRealPerCent(Complex[], double) - Static method in class woSource.math.Complex

isRealperCent(double) - Method in class woSource.math.Complex

isShort - Variable in class woSource.math.ArrayDisplay

isVisible() - Method in class woSource.math.ArrayDisplay

isWoodSample - Variable in class woSource.AirwaySegm

isZero(Complex) - Static method in class woSource.math.Complex

isZero() - Method in class woSource.math.Complex

J

JAMAsolve(double[][], double[]) - Static method in class woSource.math.OptMath

K

kernelHitsChestWall(NoduleCandidate, float[][][]) - Method in class woSource.LIDCreview

keyPressed(KeyEvent) - Method in class woSource.GenericRecallableDialog

the keyboard input (arrow keys) will be caught by whichever button has the current focus, but will affect the scrollbar last touched.

keyPressed(KeyEvent) - Method in class woSource.ScreenSelectorCanvas

note that hitting the arrow keys will increment the active window automatically.

keyPressed(KeyEvent) - Method in class woSource.ScreenSelectorClass

keyReleased(KeyEvent) - Method in class woSource.ScreenSelectorCanvas

keyTyped(KeyEvent) - Method in class woSource.ScreenSelectorCanvas

killRoi() - Method in class woSource.math.ArrayDisplay

krads - Variable in class woSource.noduleDetectionModule

L

L - Static variable in class woSource.ImageRegistrationPS

Label - Variable in class woSource.DoseReader

Label - Variable in class woSource.DoseReader_Oct2012_oldUR

Label - Variable in class woSource.FEelemClass

Label - Variable in class woSource.FEmeshClass

Label - Variable in class woSource.FEnodeClass

Label - Variable in class woSource.ImageRegistrationPS

Label - Variable in class woSource.InteractiveSnake

Label - Variable in class woSource.InteractiveSnake.Snake

Label - Variable in class woSource.math.ArrayDisplay

Label - Variable in class woSource.math.HeartLongAxis

Label - Variable in class woSource.math.Image3Dinfo

Label - Variable in class woSource.math.SeriesImagesClass

Label - Variable in class woSource.math.SimTagImageInfo

Label - Variable in class woSource.math.VesselTree

Label - Variable in class woSource.WindowLevelAdjuster

LAbodyMask - Variable in class woSource.PulmonaryTrunkSegm

LAmaskAd - Variable in class woSource.PulmonaryTrunkSegm

LASeedx - Variable in class woSource.PulmonaryTrunkSegm

LASeedy - Variable in class woSource.PulmonaryTrunkSegm

LASeedz - Variable in class woSource.PulmonaryTrunkSegm

LAselectedRoi - Variable in class woSource.HeartSegm

lastEdgePts - Variable in class woSource.InteractiveSnake.Snake

LAvesselsegm - Variable in class woSource.PulmonaryTrunkSegm

leftAtriumMask - Variable in class woSource.VesselSegm

leftAtriumSeedx - Variable in class woSource.VesselSegm

leftAtriumSeedy - Variable in class woSource.VesselSegm

leftAtriumSeedz - Variable in class woSource.VesselSegm

leftLung - Variable in class woSource.humanLungSegm

length() - Method in class woSource.math.Point2D

length() - Method in class woSource.math.Point3D

length() - Method in class woSource.math.Point4D

length() - Method in class woSource.math.Point4Dint

length - Variable in class woSource.math.VesselBranch

LesionFinder - Class in woSource

LesionFinder() - Constructor for class woSource.LesionFinder

level - Variable in class woSource.math.VesselBranch

LIDCnodule - Class in woSource.math

LIDCnodule() - Constructor for class woSource.math.LIDCnodule

LIDCnodule(LIDCnodule) - Constructor for class woSource.math.LIDCnodule

LIDCnodule(String, int, float, int, float, float, float) - Constructor for class woSource.math.LIDCnodule

LIDCnodule(String) - Constructor for class woSource.math.LIDCnodule

LIDCreview - Class in woSource

LIDCreview() - Constructor for class woSource.LIDCreview

LIDCtruthOpt - Class in woSource

LIDCtruthOpt() - Constructor for class woSource.LIDCtruthOpt

line_sep(float[], float[], float[]) - Static method in class woSource.math.MathII

line_sep2D(float, float, float[], float[]) - Static method in class woSource.math.MathII

sep between the infinitely long line passing through the 2 points and the 2D test point (positive number)

line_sep2D(float[], float[], float[]) - Static method in class woSource.math.MathII

lineSegment_sep2DlessThanThresh(float, float, float[], float[], float) - Static method in class woSource.math.MathII

sep between the line segment passing through the 2 points and the 2D test point (positive number).

linRegrSlope(float[]) - Static method in class woSource.math.ArraysI

linear regression: y = ax + b, assume x=0,1,2,...,N-1, returns values[2]

listChildren() - Method in class woSource.math.VesselBranch

listPoints() - Method in class woSource.math.VesselBranch

LMT - Static variable in class woSource.ImageRegistrationPS

ln(double) - Static method in class woSource.math.MathI

ln(float) - Static method in class woSource.math.MathI

loadKernelFromFile3D() - Method in class woSource.create3DTemplate

location - Variable in class woSource.DicomAnon

log() - Method in class woSource.math.Complex

log(Complex) - Static method in class woSource.math.Complex

log(double) - Static method in class woSource.math.MathI

log(float) - Static method in class woSource.math.MathI

log10(double) - Static method in class woSource.math.MathI

lame java math lib doesn't even have log_base_10

log10(float) - Static method in class woSource.math.MathI

loopLocs - Variable in class woSource.VesselSegm

loopThroughSlices() - Method in class woSource.math.ArrayDisplay

loopThroughSlices(int) - Method in class woSource.math.ArrayDisplay

lunggd - Variable in class woSource.humanLungSegm

lungMask - Variable in class woSource.humanLungSegm

lungMask - Variable in class woSource.lungSnake

lungMaskByte - Variable in class woSource.humanLungSegm

lungRect - Variable in class woSource.AirwaySegm

lungRect - Variable in class woSource.PulmonaryTrunkSegm

lungROI - Variable in class woSource.humanLungSegm

lungSnake - Class in woSource

lungSnake(boolean[][][], float) - Constructor for class woSource.lungSnake

lungSnake() - Constructor for class woSource.noduleDetection.lungSnake

LVSeedx - Variable in class woSource.PulmonaryTrunkSegm

LVSeedy - Variable in class woSource.PulmonaryTrunkSegm

LVSeedz - Variable in class woSource.PulmonaryTrunkSegm

M

M - Static variable in class woSource.ImageRegistrationPS

main(String[]) - Static method in class woSource.NNLSSolver

In case you want to test the solver, there is this handy-dandy testing function.

makeConst(short[], int) - Static method in class woSource.math.ArraysI

makeConst(short[][], int) - Static method in class woSource.math.ArraysI

makeConst(short[][][], int) - Static method in class woSource.math.ArraysI

makeSparse(boolean[][][], float, float) - Static method in class woSource.math.ImgProc

WO 8/15/2012 intent is to take a binary image with a high density of points and remove many adjacent points, creating a more sparse version.

maskBadBaselineVals() - Method in class woSource.DTIanalysis

maskDepth - Variable in class woSource.math.VesselTree

maskHeight - Variable in class woSource.math.VesselTree

maskImg - Variable in class woSource.math.SeriesImagesClass

MaskPixelsOverlay(boolean[][]) - Method in class woSource.math.ArrayDisplay

masksWereSaved - Variable in class woSource.PulmonaryTrunkSegm

masksWereSaved - Variable in class woSource.VesselSegm

maskWasVoided - Variable in class woSource.math.HyperSkelPair

maskWidth - Variable in class woSource.math.VesselTree

matchXYscales - Variable in class woSource.ImageRegistration

MathI - Class in woSource.math

WO class of basic math operations.

MathI() - Constructor for class woSource.math.MathI

MathII - Class in woSource.math

My library of high math functions including vectors.

MathII() - Constructor for class woSource.math.MathII

matrix_inv(float[][]) - Static method in class woSource.math.ArraysI

matrix inverse using the JAMA library

matrix_inv(double[][]) - Static method in class woSource.math.ArraysI

matrix inverse using the JAMA library

max(byte[][], byte[][]) - Static method in class woSource.math.ArraysI

resultant array is element-wise max between A's and B's elements

max(byte[][][], byte[][][]) - Static method in class woSource.math.ArraysI

resultant array is element-wise max between A's and B's elements

max(short[][], short[][]) - Static method in class woSource.math.ArraysI

resultant array is element-wise max between A's and B's elements

max(short[][][], short[][][]) - Static method in class woSource.math.ArraysI

resultant array is element-wise max between A's and B's elements

max(float[][], float[][]) - Static method in class woSource.math.ArraysI

resultant array is element-wise max between A's and B's elements

max(float[][][], float[][][]) - Static method in class woSource.math.ArraysI

resultant array is element-wise max between A's and B's elements

max(byte[]) - Static method in class woSource.math.ArraysI

max(byte[], int) - Static method in class woSource.math.ArraysI

max(byte[], int, int) - Static method in class woSource.math.ArraysI

max(byte[][]) - Static method in class woSource.math.ArraysI

max(byte[][], int, int) - Static method in class woSource.math.ArraysI

max(byte[][][]) - Static method in class woSource.math.ArraysI

max(byte[][][], int, int, int) - Static method in class woSource.math.ArraysI

max(byte[][][][]) - Static method in class woSource.math.ArraysI

max(byte[][][][], int, int, int, int) - Static method in class woSource.math.ArraysI

max(short[]) - Static method in class woSource.math.ArraysI

max(short[], int) - Static method in class woSource.math.ArraysI

max(short[], int, int) - Static method in class woSource.math.ArraysI

max(short[][]) - Static method in class woSource.math.ArraysI

max(short[][], int, int, int, int) - Static method in class woSource.math.ArraysI

max(short[][], int, int) - Static method in class woSource.math.ArraysI

max(short[][][]) - Static method in class woSource.math.ArraysI

max(short[][][], int, int, int) - Static method in class woSource.math.ArraysI

max(short[][][][]) - Static method in class woSource.math.ArraysI

max(short[][][][], int, int, int, int) - Static method in class woSource.math.ArraysI

max(int[]) - Static method in class woSource.math.ArraysI

max(int[], int) - Static method in class woSource.math.ArraysI

max(int[], int, int) - Static method in class woSource.math.ArraysI

max(int[][]) - Static method in class woSource.math.ArraysI

max(int[][], int, int) - Static method in class woSource.math.ArraysI

max(int[][][]) - Static method in class woSource.math.ArraysI

max(int[][][], int, int, int) - Static method in class woSource.math.ArraysI

max(int[][][][]) - Static method in class woSource.math.ArraysI

max(int[][][][], int, int, int, int) - Static method in class woSource.math.ArraysI

max(float[]) - Static method in class woSource.math.ArraysI

max(float[], int) - Static method in class woSource.math.ArraysI

max(float[], int, int) - Static method in class woSource.math.ArraysI

max(float[][]) - Static method in class woSource.math.ArraysI

max(float[][], int, int) - Static method in class woSource.math.ArraysI

max(float[][][]) - Static method in class woSource.math.ArraysI

max(float[][][], int, int, int) - Static method in class woSource.math.ArraysI

max(double[]) - Static method in class woSource.math.ArraysI

max(double[], int) - Static method in class woSource.math.ArraysI

max(double[], int, int) - Static method in class woSource.math.ArraysI

max(double[][]) - Static method in class woSource.math.ArraysI

max(double[][], int, int) - Static method in class woSource.math.ArraysI

max(double[][][]) - Static method in class woSource.math.ArraysI

max(double[][][], int, int, int) - Static method in class woSource.math.ArraysI

max(Point2D[]) - Static method in class woSource.math.ArraysI

max(Point2D[][]) - Static method in class woSource.math.ArraysI

max(Point2D[][][]) - Static method in class woSource.math.ArraysI

max(Point3D[]) - Static method in class woSource.math.ArraysI

max(Point3D[][]) - Static method in class woSource.math.ArraysI

max(Point3D[][][]) - Static method in class woSource.math.ArraysI

max(int, int) - Static method in class woSource.math.MathI

max(float, float) - Static method in class woSource.math.MathI

max(double, double) - Static method in class woSource.math.MathI

max(float, float, float) - Static method in class woSource.math.MathI

max(float, float, float, float) - Static method in class woSource.math.MathI

max(int, int, int) - Static method in class woSource.math.MathI

maxActiveBranchIndex - Variable in class woSource.math.VesselTree

maxBrLength - Variable in class woSource.math.VesselTree

maxBrRadius - Variable in class woSource.math.VesselTree

maxBrTort - Variable in class woSource.math.VesselTree

maxDiff - Variable in class woSource.seededRegionGrowing

maxDiff - Variable in class woSource.VesselSegm

maxImgHeight - Variable in class woSource.HeartSegm

maxImgWidth - Variable in class woSource.HeartSegm

maxIndex(int[]) - Static method in class woSource.math.ArraysI

return index to max value in array

maxIndex(int[], int) - Static method in class woSource.math.ArraysI

maxIndex(int[], int, int) - Static method in class woSource.math.ArraysI

maxIndex(float[]) - Static method in class woSource.math.ArraysI

maxIndex(float[], int) - Static method in class woSource.math.ArraysI

maxIndex(float[], int, int) - Static method in class woSource.math.ArraysI

maxInitBranches - Variable in class woSource.math.VesselTree

maxNNodes - Variable in class woSource.math.VesselBranch

maxPathLength - Variable in class woSource.math.VesselTree

maxpt(Point2D[]) - Static method in class woSource.math.ArraysI

maxpt(Point2D[], int, int) - Static method in class woSource.math.ArraysI

maxpt(Point2D[][]) - Static method in class woSource.math.ArraysI

maxpt(Point2D[][], int, int, int, int) - Static method in class woSource.math.ArraysI

maxpt(Point3D[]) - Static method in class woSource.math.ArraysI

maxpt(Point3D[], int, int) - Static method in class woSource.math.ArraysI

maxpt(Point3Dint[]) - Static method in class woSource.math.ArraysI

maxpt(Point3Dint[], int, int) - Static method in class woSource.math.ArraysI

maxpt(Point4D[]) - Static method in class woSource.math.ArraysI

maxpt(Point4D[], int, int) - Static method in class woSource.math.ArraysI

maxpt(int[][]) - Static method in class woSource.math.ArraysI

maxpt(int[][], int, int, int, int) - Static method in class woSource.math.ArraysI

maxpt(short[][]) - Static method in class woSource.math.ArraysI

maxpt(short[][], int, int, int, int) - Static method in class woSource.math.ArraysI

maxpt(float[][]) - Static method in class woSource.math.ArraysI

maxpt(float[][], int, int, int, int) - Static method in class woSource.math.ArraysI

maxpt(int[][][]) - Static method in class woSource.math.ArraysI

maxpt(int[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

maxpt(byte[][][]) - Static method in class woSource.math.ArraysI

maxpt(byte[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

maxpt(short[][][]) - Static method in class woSource.math.ArraysI

maxpt(short[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

maxpt(float[][][]) - Static method in class woSource.math.ArraysI

maxpt(float[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

maxpt(NoduleCandidate[]) - Static method in class woSource.math.ArraysI

maxpt(NoduleCandidate[], int, int) - Static method in class woSource.math.ArraysI

maxPts - Variable in class woSource.math.VesselBranch

maxSlices - Variable in class woSource.HeartSegm

maxthresh - Variable in class woSource.AirwaySegm

maxthresh - Variable in class woSource.PulmonaryTrunkSegm

maxTimes - Variable in class woSource.HeartSegm

maxval - Variable in class woSource.math.ArrayDisplay

maxVoxelCount - Variable in class woSource.seededRegionGrowing

maxVoxelCount - Variable in class woSource.VesselSegm

mean(Complex[]) - Static method in class woSource.math.Complex

mediastinumMask - Variable in class woSource.VesselSegm

midSeptumPt - Variable in class woSource.math.HeartLongAxis

midSeptumTheta - Variable in class woSource.math.HeartLongAxis

min(byte[]) - Static method in class woSource.math.ArraysI

min(byte[], int) - Static method in class woSource.math.ArraysI

min(byte[], int, int) - Static method in class woSource.math.ArraysI

min(short[]) - Static method in class woSource.math.ArraysI

min(short[], int) - Static method in class woSource.math.ArraysI

min(short[], int, int) - Static method in class woSource.math.ArraysI

min(int[]) - Static method in class woSource.math.ArraysI

min(int[], int) - Static method in class woSource.math.ArraysI

min(int[], int, int) - Static method in class woSource.math.ArraysI

min(float[]) - Static method in class woSource.math.ArraysI

min(float[], int) - Static method in class woSource.math.ArraysI

min(float[], int, int) - Static method in class woSource.math.ArraysI

min(double[]) - Static method in class woSource.math.ArraysI

min(double[], int) - Static method in class woSource.math.ArraysI

min(double[], int, int) - Static method in class woSource.math.ArraysI

min(byte[][]) - Static method in class woSource.math.ArraysI

min(short[][]) - Static method in class woSource.math.ArraysI

min(int[][]) - Static method in class woSource.math.ArraysI

min(float[][]) - Static method in class woSource.math.ArraysI

min(double[][]) - Static method in class woSource.math.ArraysI

min(byte[][][]) - Static method in class woSource.math.ArraysI

min(short[][][]) - Static method in class woSource.math.ArraysI

min(int[][][]) - Static method in class woSource.math.ArraysI

min(float[][][]) - Static method in class woSource.math.ArraysI

min(double[][][]) - Static method in class woSource.math.ArraysI

min(byte[][][][]) - Static method in class woSource.math.ArraysI

min(short[][][][]) - Static method in class woSource.math.ArraysI

min(int[][][][]) - Static method in class woSource.math.ArraysI

min(Point2D[]) - Static method in class woSource.math.ArraysI

min(Point2D[][]) - Static method in class woSource.math.ArraysI

min(Point2D[][][]) - Static method in class woSource.math.ArraysI

min(Point3D[]) - Static method in class woSource.math.ArraysI

min(Point3D[][]) - Static method in class woSource.math.ArraysI

min(Point3D[][][]) - Static method in class woSource.math.ArraysI

min(float, float, float) - Static method in class woSource.math.MathI

min(float, float, float, float) - Static method in class woSource.math.MathI

min(int, int, int) - Static method in class woSource.math.MathI

min(int, int) - Static method in class woSource.math.MathI

min(float, float) - Static method in class woSource.math.MathI

min(double, double) - Static method in class woSource.math.MathI

minBranchLength - Variable in class woSource.math.VesselTree

minpt(Point2D[]) - Static method in class woSource.math.ArraysI

minpt(Point2D[], int, int) - Static method in class woSource.math.ArraysI

minpt(Point2D[][]) - Static method in class woSource.math.ArraysI

minpt(Point2D[][], int, int, int, int) - Static method in class woSource.math.ArraysI

minpt(int[][]) - Static method in class woSource.math.ArraysI

minpt(int[][], int, int, int, int) - Static method in class woSource.math.ArraysI

minpt(float[][]) - Static method in class woSource.math.ArraysI

minpt(float[][], int, int, int, int) - Static method in class woSource.math.ArraysI

minpt(int[][][]) - Static method in class woSource.math.ArraysI

minpt(int[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

minpt(float[][][]) - Static method in class woSource.math.ArraysI

minpt(float[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

minthresh - Variable in class woSource.PulmonaryTrunkSegm

minthresh - Variable in class woSource.seededRegionGrowing

minthresh - Variable in class woSource.VesselSegm

minus(Point3Dint, Point3Dint) - Static method in class woSource.math.ArraysI

create vector separating the 2 Points

minus(byte[][], byte[][]) - Static method in class woSource.math.ArraysI

resultant array is element-wise subtraction of B's from A's elements.

minus(byte[][][], byte[][][]) - Static method in class woSource.math.ArraysI

minus(Complex, Complex) - Static method in class woSource.math.Complex

minus(Complex, double) - Static method in class woSource.math.Complex

minus(double, Complex) - Static method in class woSource.math.Complex

minus(double, double) - Static method in class woSource.math.Complex

minus(Complex) - Method in class woSource.math.Complex

minus(double) - Method in class woSource.math.Complex

minusEquals(Complex) - Method in class woSource.math.Complex

minusEquals(double) - Method in class woSource.math.Complex

minusInfinity() - Static method in class woSource.math.Complex

minusJay() - Static method in class woSource.math.Complex

minusOne() - Static method in class woSource.math.Complex

minval - Variable in class woSource.math.ArrayDisplay

MIPcalcStruc() - Constructor for class woSource.math.ImgProc.MIPcalcStruc

MIPs_canvas - Static variable in class woSource.MIPSviewer

MIPSviewer - Class in woSource

WO 11/11/2011-1/2013 implements a user-interactive Maximum Intentisy Projection (MIP) viewer

MIPSviewer() - Constructor for class woSource.MIPSviewer

MIPSviewer.Updater - Class in woSource

MIPSviewerColor - Class in woSource

WO color version added 1/2013.

MIPSviewerColor() - Constructor for class woSource.MIPSviewerColor

mitralValveFocalPt - Variable in class woSource.math.HeartLongAxis

mmPerPixelX - Variable in class woSource.DoseReader

mmPerPixelX - Variable in class woSource.math.ArrayDisplay

mmPerPixelXY - Variable in class woSource.lungSnake

mmPerPixelXY - Variable in class woSource.math.VesselBranch

mmPerPixelXY - Variable in class woSource.math.VesselTree

mmPerPixelY - Variable in class woSource.DoseReader

mmPerPixelY - Variable in class woSource.math.ArrayDisplay

mmPerPixelZ - Variable in class woSource.math.VesselBranch

mmPerPixelZ - Variable in class woSource.math.VesselTree

mmPPxy - Variable in class woSource.math.Image3Dinfo

mmPPz - Variable in class woSource.math.Image3Dinfo

MonteDoseSpread(int) - Method in class woSource.DoseCalc

MotionBlur - Class in woSource

MotionBlur() - Constructor for class woSource.MotionBlur

motionBlurKernel(int, int) - Static method in class woSource.math.MathII

mouseDragged(MouseEvent) - Method in class woSource.MIPSviewer

mouseDragged(MouseEvent) - Method in class woSource.MouseMicroCTlungSegm

mouseDragged(MouseEvent) - Method in class woSource.Point3Dviewer

mouseDragged(MouseEvent) - Method in class woSource.ScreenSelectorCanvas

mouseDragged(MouseEvent) - Method in class woSource.ScreenSelectorClass

MouseLungSegmentor - Class in woSource

MouseLungSegmentor() - Constructor for class woSource.MouseLungSegmentor

MouseMicroCTlungSegm - Class in woSource

MouseMicroCTlungSegm() - Constructor for class woSource.MouseMicroCTlungSegm

mouseMoved(MouseEvent) - Method in class woSource.MIPSviewer

mouseMoved(MouseEvent) - Method in class woSource.Point3Dviewer

mouseMoved(MouseEvent) - Method in class woSource.ScreenSelectorCanvas

mouseMoved(MouseEvent) - Method in class woSource.ScreenSelectorClass

mousePressed(MouseEvent) - Method in class woSource.MIPSviewer

mousePressed(MouseEvent) - Method in class woSource.Point3Dviewer

mousePressed(MouseEvent) - Method in class woSource.ScreenSelectorCanvas

mousePressed(MouseEvent) - Method in class woSource.ScreenSelectorClass

mouseReleased(MouseEvent) - Method in class woSource.MIPSviewer

mouseReleased(MouseEvent) - Method in class woSource.Point3Dviewer

mouseReleased(MouseEvent) - Method in class woSource.ScreenSelectorCanvas

mouseReleased(MouseEvent) - Method in class woSource.ScreenSelectorClass

ms2MinSec(long) - Static method in class woSource.math.MathI

mult(byte[][], int) - Static method in class woSource.math.ArraysI

matrix multiplication by scalar.

mult(byte[][][], int) - Static method in class woSource.math.ArraysI

matrix multiplication by scalar

mult(byte[][], float) - Static method in class woSource.math.ArraysI

matrix multiplication by scalar

mult(byte[][][], float) - Static method in class woSource.math.ArraysI

matrix multiplication by scalar

mult(short[][], int) - Static method in class woSource.math.ArraysI

matrix multiplication by scalar

mult(short[][][], int) - Static method in class woSource.math.ArraysI

matrix multiplication by scalar

mult(short[][][][], int) - Static method in class woSource.math.ArraysI

mult(float[], int) - Static method in class woSource.math.ArraysI

mult(float[][], int) - Static method in class woSource.math.ArraysI

mult(float[][][], int) - Static method in class woSource.math.ArraysI

mult(float[][][][], int) - Static method in class woSource.math.ArraysI

mult(float[], float) - Static method in class woSource.math.ArraysI

mult(float[][], float) - Static method in class woSource.math.ArraysI

mult(float[][][], float) - Static method in class woSource.math.ArraysI

mult(float[][][][], float) - Static method in class woSource.math.ArraysI

mult(float[][], float[]) - Static method in class woSource.math.ArraysI

does post-vec mult

mult(float[], float[][]) - Static method in class woSource.math.ArraysI

pre-mult as needed after creating rotation matrix getRotMtx() below

mult(float[][], float[][]) - Static method in class woSource.math.ArraysI

mult(float[][][], float[][]) - Static method in class woSource.math.ArraysI

mult(double[], double[][]) - Static method in class woSource.math.ArraysI

mult(double[][], double[]) - Static method in class woSource.math.ArraysI

mult(double[][], double[][]) - Static method in class woSource.math.ArraysI

mult(double[][][], double[][]) - Static method in class woSource.math.ArraysI

multFt(float[][], float[][]) - Static method in class woSource.math.MathII

multiplication of complex fourier transforms using WO-NR conventions

multFt(short[][][], float[][][]) - Static method in class woSource.math.MathII

multFt(float[][][], short[][][]) - Static method in class woSource.math.MathII

multFt(float[][][], float[][][]) - Static method in class woSource.math.MathII

multvec(float[][], float[][]) - Static method in class woSource.math.ArraysI

intended for transformation (rotation) of array of point vectors alters the inputted B array -- to save memory

multvec(float[][], float[][][]) - Static method in class woSource.math.ArraysI

intended for transformation (rotation) of array of point vectors alters the inputted B array -- to save memory

multvec(float[][], float[][][][]) - Static method in class woSource.math.ArraysI

intended for transformation (rotation) of array of point vectors alters the inputted B array -- to save memory

myIndex - Variable in class woSource.math.VesselBranch

myOptThread(int, int, String) - Constructor for class woSource.noduleDetectionModule.myOptThread

myThread(int, int, String) - Constructor for class woSource.noduleDetection.myThread

N

name_ext - Variable in class woSource.noduleDetectionModule

name_ext - Variable in class woSource.PulmonaryTrunkSegm

name_ext - Variable in class woSource.RatImageAdjuster

name_ext - Variable in class woSource.VesselSegm

nameSorter(String[]) - Static method in class woSource.math.ArraysI

a version of 'quicksort'

NangleSteps - Variable in class woSource.math.VesselBranch

nBranches - Variable in class woSource.math.VesselTree

nbrOn(boolean[][]) - Static method in class woSource.math.ArraysI

WO 7/9/2013 return number of On pixels = volume of object if objects is connected ala a flood-fill

nbrOn(boolean[][][]) - Static method in class woSource.math.ArraysI

NCCCoptLoc(int, int) - Method in class woSource.LIDCreview

NCCCoptLoc(int, int) - Method in class woSource.noduleDetection

NCCCoptLoc(int, int) - Method in class woSource.noduleDetectionModule

NCCCoptPadding(int, int) - Method in class woSource.noduleDetection

NCCCoptPadding(int, int) - Method in class woSource.noduleDetectionModule

NCCCoptRadii(int, int, int) - Method in class woSource.LIDCreview

public NoduleCandidate NCCCtestRadPad(NoduleCandidate candAt, float radAt, float padAt) { // find best match using in-between-sized templates // with iter, permit smaller increments in opt radius float[][][][] kall = new float[MathI.round(sliceThickness)][1][1][1]; byte[][][] corrAll; // will process together the 3 shifts at each krad Point3D bestFitLoc3D = new Point3D(); NoduleCandidate bestFitLoc = new NoduleCandidate(); float dd,ww,hh; float orig_slice; // ArraysI.print(zoomRads," zoomrads for cand "+c); dd = candAt.sliceI-(float)MathI.round(candAt.sliceI); ww = candAt.x-(float)MathI.round(candAt.x); hh = candAt.y-(float)MathI.round(candAt.y); kall = calcKall(radAt, padAt, sliceThickness, mmPerPixelX, mmPerPixelY, /* impart the shifts ** dd,ww,hh); // check in 3x5x5 cube around current point and within LungMask // invoke non-// version corrAll = ImgProc.statsCorrCirc(origimg, kall, lungMask, MathI.round(candAt.sliceI)-1, MathI.round(candAt.x)-2, MathI.round(candAt.y)-2, MathI.round(candAt.sliceI)+1, MathI.round(candAt.x)+2, MathI.round(candAt.y)+2); bestFitLoc3D = ArraysI.maxpt(corrAll); bestFitLoc3D.x -= dd; bestFitLoc3D.y -= ww; bestFitLoc3D.z -= hh; bestFitLoc = new NoduleCandidate(candAt.patientID, bestFitLoc3D.x, bestFitLoc3D.y, bestFitLoc3D.z, radAt, padAt, bestFitLoc3D.value); IJ.log(" best rad/pad combo for cand "+candAt+": "+bestFitLoc); return bestFitLoc; } // end test a radius/padding combo

NCCCoptRadii(int, int, int) - Method in class woSource.noduleDetection

NCCCoptRadii(int, int, int) - Method in class woSource.noduleDetectionModule

nChildren - Variable in class woSource.math.VesselBranch

nConPts - Variable in class woSource.HeartSegm

nContourPts - Variable in class woSource.ContourFit

negate(Complex) - Static method in class woSource.math.Complex

negate() - Method in class woSource.math.Complex

neighborMult(int[][]) - Static method in class woSource.math.ImgProc

meant to weigh condense-ness in 2D histogram

neighborProbMult(int[][]) - Static method in class woSource.math.ImgProc

NelemNodes - Variable in class woSource.FEelemClass

Nelems - Variable in class woSource.FEmeshClass

Nextrema - Variable in class woSource.noduleDetectionModule

nfound - Variable in class woSource.lungSnake

NinterPts - Variable in class woSource.InteractiveSnake.SmoothSnake

NinterPts - Variable in class woSource.math.VesselBranch

nLevels - Variable in class woSource.math.VesselTree

nLoopPts - Variable in class woSource.math.VesselTree

nLoopPts - Variable in class woSource.VesselSegm

NMAX - Variable in class woSource.InteractiveSnake.Snake

NMI(short[][][], short[][][], int, int, int) - Static method in class woSource.math.ImgProc

compute mutual information index at A[az][ax][ay]
assume A&B are already scaled 0..255

NMI(short[][][], short[][][]) - Static method in class woSource.math.ImgProc

compute for each pixel in A image
WO: extend A-array with zeros to cover all part where B extends outside the A boundaries.

NNLSSolver - Class in woSource

This is a perfectly functional Java NNLS solver that utilizes JAMA for all the Matrix calculations.

NNLSSolver() - Constructor for class woSource.NNLSSolver

Nnodes - Variable in class woSource.FEmeshClass

nnodes - Variable in class woSource.math.VesselBranch

NodDetThread(int, int, int) - Constructor for class woSource.noduleDetectionModule.NodDetThread

NodeElems - Variable in class woSource.FEnodeClass

Nodes - Variable in class woSource.FEmeshClass

Nodes - Variable in class woSource.math.VesselBranch

NoduleCandidate - Class in woSource.math

NoduleCandidate() - Constructor for class woSource.math.NoduleCandidate

NoduleCandidate(NoduleCandidate) - Constructor for class woSource.math.NoduleCandidate

NoduleCandidate(String, float, float, float, float, float, float) - Constructor for class woSource.math.NoduleCandidate

NoduleCandidate(String) - Constructor for class woSource.math.NoduleCandidate

noduleDetection - Class in woSource

noduleDetection() - Constructor for class woSource.noduleDetection

noduleDetection.lungSnake - Class in woSource

WO 9/23/2013 this whole part needs to be recoded to use humanLungSegm

noduleDetection.myThread - Class in woSource

noduleDetectionModule - Class in woSource

WO 7/31/2012, This is the version of NoduleDetection that runs when the user selects nodule detection from the Main Menu -> Process tab.

noduleDetectionModule() - Constructor for class woSource.noduleDetectionModule

noduleDetectionModule.myOptThread - Class in woSource

noduleDetectionModule.NodDetThread - Class in woSource

noImageToDisplay - Variable in class woSource.ScreenSelectorCanvas

Nopt_calls - Variable in class woSource.math.OptMath

normal - Variable in class woSource.InteractiveSnake.Snake

normalize(float[][]) - Static method in class woSource.math.ArraysI

normalizes an array's values (e.g.

normalize(float[][][]) - Static method in class woSource.math.ArraysI

normalize(double[][]) - Static method in class woSource.math.ArraysI

normalize(double[][][]) - Static method in class woSource.math.ArraysI

NormalizedBeadProfile(int, float) - Static method in class woSource.math.MathII

returns values 0..1, 1.0 at center of bead

nOrphanedBranches - Variable in class woSource.VesselSegm

nPhiPts - Variable in class woSource.math.VesselBranch

npoints - Variable in class woSource.math.Polygon2D

npoints - Variable in class woSource.math.Polygon3D

npoints - Variable in class woSource.math.Polygon3Dint

nProcessTimes - Variable in class woSource.HeartSegm

NPT - Variable in class woSource.InteractiveSnake.Snake

Npts - Variable in class woSource.InteractiveSnake.SmoothSnake

npts - Variable in class woSource.math.VesselBranch

NRfour1(float[], int, int) - Static method in class woSource.math.MathII

NRrealft(float[], int, int) - Static method in class woSource.math.MathII

Num.

nSeries - Variable in class woSource.HeartSegm

nSlices - Variable in class woSource.HeartSegm

nSlices - Variable in class woSource.math.Image3Dinfo

nSlices - Variable in class woSource.WindowLevelAdjuster

nsmpts - Variable in class woSource.math.VesselBranch

nSmPtsPerElement - Variable in class woSource.math.VesselBranch

nSnakes - Variable in class woSource.InteractiveSnake.SnakeStack

nterms - Variable in class woSource.ContourFit

nthRoot(int) - Method in class woSource.math.Complex

nthRoot(Complex, int) - Static method in class woSource.math.Complex

ntimes - Variable in class woSource.ContourFit

nTimes - Variable in class woSource.math.Image3Dinfo

ntreeTops - Variable in class woSource.PulmonaryTrunkSegm

numberToByteArray(String, int) - Method in class woSource.DicomAnon

Nvars - Variable in class woSource.math.OptMath

O

oddLocations - Variable in class woSource.DicomAnon

oneDarray(int) - Static method in class woSource.math.Complex

oneDarray(int, double, double) - Static method in class woSource.math.Complex

oneDarray(int, Complex) - Static method in class woSource.math.Complex

OneMainBranch - Variable in class woSource.math.VesselTree

ones(byte[]) - Static method in class woSource.math.ArraysI

returns entire matrix of 255 of same dims as A

ones(byte[][]) - Static method in class woSource.math.ArraysI

returns entire matrix of 255 of same dims as A

ones(byte[][][]) - Static method in class woSource.math.ArraysI

returns entire matrix of 255 of same dims as A

ones(int[]) - Static method in class woSource.math.ArraysI

returns entire matrix of ones of same dims as A

ones(float[]) - Static method in class woSource.math.ArraysI

returns entire matrix of ones of same dims as A

ones(float[][]) - Static method in class woSource.math.ArraysI

ones(float[][][]) - Static method in class woSource.math.ArraysI

onlyOneImage - Variable in class woSource.math.ArrayDisplay

openOp(byte[][], int) - Static method in class woSource.math.ImgProc

binary image operation Open = dilate(erode(A))

openOp(byte[][], int, Rectangle) - Static method in class woSource.math.ImgProc

openOp(byte[][][], int) - Static method in class woSource.math.ImgProc

openOp(byte[][][], int, Rectangle3D) - Static method in class woSource.math.ImgProc

openOp(byte[][][], int, float) - Static method in class woSource.math.ImgProc

openOp(byte[][][], int, float, Rectangle3D) - Static method in class woSource.math.ImgProc

openOp(byte[][], float) - Static method in class woSource.math.ImgProc

openOp(byte[][], float, Rectangle) - Static method in class woSource.math.ImgProc

openOp(byte[][][], float) - Static method in class woSource.math.ImgProc

openOp(byte[][][], float, Rectangle3D) - Static method in class woSource.math.ImgProc

openOp(byte[][][], float, float) - Static method in class woSource.math.ImgProc

openOp(byte[][][], float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

openOp(boolean[][], int) - Static method in class woSource.math.ImgProc

openOp(boolean[][], int, Rectangle) - Static method in class woSource.math.ImgProc

openOp(boolean[][][], int) - Static method in class woSource.math.ImgProc

openOp(boolean[][][], int, Rectangle3D) - Static method in class woSource.math.ImgProc

openOp(boolean[][][], int, float) - Static method in class woSource.math.ImgProc

openOp(boolean[][][], int, float, Rectangle3D) - Static method in class woSource.math.ImgProc

openOp(boolean[][], float) - Static method in class woSource.math.ImgProc

openOp(boolean[][], float, Rectangle) - Static method in class woSource.math.ImgProc

openOp(boolean[][][], float) - Static method in class woSource.math.ImgProc

openOp(boolean[][][], float, Rectangle3D) - Static method in class woSource.math.ImgProc

openOp(boolean[][][], float, float) - Static method in class woSource.math.ImgProc

openOp(boolean[][][], float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

openOp(boolean[][][], float, float, boolean[][][]) - Static method in class woSource.math.ImgProc

OptBranchNode(int, int, int) - Method in class woSource.math.VesselTree

optimize over each node's 6 parameters X,Y,Z, DXDS, DYDS, DZDS driven by NCCC to the original image,
If at the first node and the branch has a parent then do not opt over the coord params because those are already being optimized when the parent's last node's coords are optimized.

OptBranchRadius(int, int) - Method in class woSource.math.VesselTree

optimize over the branch radius, driven by NCCC to the original image.

OptBranchTaper(int, int) - Method in class woSource.math.VesselTree

optimize over the branch radius taper, driven by NCCC to the original image.

OptBrNodThread(int, int, int) - Constructor for class woSource.math.VesselTree.OptBrNodThread

OptBrRadThread(int, int, int) - Constructor for class woSource.math.VesselTree.OptBrRadThread

optimizeOverCands() - Method in class woSource.noduleDetectionModule

optLikelihood() - Method in class woSource.LIDCtruthOpt

OptMath - Class in woSource.math

OptMath() - Constructor for class woSource.math.OptMath

OptNodes(int) - Method in class woSource.math.VesselTree

WO 4/16/2012 parallel version.

optOver2Params(short[][], float, float, float, float) - Method in class woSource.HeartSegm

optOver3Params(short[][], float, float, float, float) - Method in class woSource.HeartSegm

optOver4Params(short[][], float, float, float, float) - Method in class woSource.HeartSegm

optParams() - Method in class woSource.LIDCreview

OptRadii(int) - Method in class woSource.math.VesselTree

WO 4/11/2012 parallel version.

optTagWarp(int) - Method in class woSource.HeartSegm

optThis - Variable in class woSource.InteractiveSnake_Hermite

optThis - Variable in class woSource.InteractiveSnake_Hermite3D

OptToImage(byte[][][]) - Method in class woSource.math.VesselTree

4/34/2013 optimize over each branch params.

OptToImage(short[][][]) - Method in class woSource.math.VesselTree

4/34/2013 optimize over each branch params.

OR(byte[][], byte[][]) - Static method in class woSource.math.ArraysI

boolean OR operator

OR(byte[][][], byte[][][]) - Static method in class woSource.math.ArraysI

OR(boolean[][], boolean[][]) - Static method in class woSource.math.ArraysI

OR(boolean[][][], boolean[][][]) - Static method in class woSource.math.ArraysI

origImg - Variable in class woSource.math.VesselTree

origImgByte - Variable in class woSource.math.VesselTree

origSelectedRoi - Variable in class woSource.InteractiveSnake

orphanedBranches - Variable in class woSource.VesselSegm

outputdir - Variable in class woSource.PulmonaryTrunkSegm

outputdir - Variable in class woSource.RatImageAdjuster

outputdir - Variable in class woSource.VesselSegm

OutputParentDir - Static variable in class woSource.math.MathI

outwardExtMax - Variable in class woSource.InteractiveSnake.Snake

over(Complex, Complex) - Static method in class woSource.math.Complex

over(Complex, double) - Static method in class woSource.math.Complex

over(double, Complex) - Static method in class woSource.math.Complex

over(double, double) - Static method in class woSource.math.Complex

over(Complex) - Method in class woSource.math.Complex

over(double) - Method in class woSource.math.Complex

overEquals(Complex) - Method in class woSource.math.Complex

overEquals(double) - Method in class woSource.math.Complex

overlay3Ddisk(int, int, int, float, float, float, float, String) - Method in class woSource.math.ArrayDisplay

intent is to draw a disk at any orientation (orX,Y,Z) in 3D; to help visualize vessels WO 8/22/2012 added ability to draw in mm if sliceCenterSep and mmPerPixelX,Y are set.

overlayArrow(float, float) - Method in class woSource.math.ArrayDisplay

overlayArrow(float, float, String) - Method in class woSource.math.ArrayDisplay

overlayBestCandTemplate() - Method in class woSource.noduleDetectionModule

overlayBox(Point3D[], int) - Method in class woSource.math.ArrayDisplay

WO created 12/23/2010 assumes each 3D point can be anywhere

overlayBox(Point3D[], int, String) - Method in class woSource.math.ArrayDisplay

overlayBox(Point4D, int) - Method in class woSource.math.ArrayDisplay

overlayBox(Point4D, int, String) - Method in class woSource.math.ArrayDisplay

overlayBox(Point4D[], int) - Method in class woSource.math.ArrayDisplay

overlayBox(Point4D[], int, String) - Method in class woSource.math.ArrayDisplay

overlayBox(NoduleCandidate[], int, int) - Method in class woSource.math.ArrayDisplay

overlayBox(NoduleCandidate[], int) - Method in class woSource.math.ArrayDisplay

overlayBox(NoduleCandidate[], int, String) - Method in class woSource.math.ArrayDisplay

overlayBox(NoduleCandidate[], int, int, String) - Method in class woSource.math.ArrayDisplay

overlayBox(NoduleCandidate, int) - Method in class woSource.math.ArrayDisplay

overlayBox(NoduleCandidate, int, String) - Method in class woSource.math.ArrayDisplay

overlayBox(LIDCnodule[], int) - Method in class woSource.math.ArrayDisplay

overlayBox(LIDCnodule[], int, String) - Method in class woSource.math.ArrayDisplay

overlayBox(LIDCnodule, int) - Method in class woSource.math.ArrayDisplay

overlayBox(LIDCnodule, int, String) - Method in class woSource.math.ArrayDisplay

overlayCircle(NoduleCandidate[], float) - Method in class woSource.math.ArrayDisplay

overlayCircle(NoduleCandidate[], float, String) - Method in class woSource.math.ArrayDisplay

overlayCircle(NoduleCandidate[], int, float, String) - Method in class woSource.math.ArrayDisplay

overlayCircle(float, float, float) - Method in class woSource.math.ArrayDisplay

assumes that the x,y passed in are meant to be the center of the circle and radius is in pixels

overlayCircle(float, float, float, String) - Method in class woSource.math.ArrayDisplay

overlayCircle(float, float, float, Color) - Method in class woSource.math.ArrayDisplay

overlayDiamond(Point4D, int) - Method in class woSource.math.ArrayDisplay

overlayDiamond(Point4D, int, String) - Method in class woSource.math.ArrayDisplay

overlayDiamond(Point4D[], int) - Method in class woSource.math.ArrayDisplay

overlayDiamond(Point4D[], int, String) - Method in class woSource.math.ArrayDisplay

overlayDiamond(NoduleCandidate, int) - Method in class woSource.math.ArrayDisplay

overlayDiamond(NoduleCandidate, int, String) - Method in class woSource.math.ArrayDisplay

overlayDiamond(NoduleCandidate[], int) - Method in class woSource.math.ArrayDisplay

overlayDiamond(NoduleCandidate[], int, String) - Method in class woSource.math.ArrayDisplay

overlayDiamond(LIDCnodule[], int) - Method in class woSource.math.ArrayDisplay

overlayDiamond(LIDCnodule[], int, String) - Method in class woSource.math.ArrayDisplay

overlayDiamond(LIDCnodule, int) - Method in class woSource.math.ArrayDisplay

overlayDiamond(LIDCnodule, int, String) - Method in class woSource.math.ArrayDisplay

overlayLine(Point2D, Point2D, String) - Method in class woSource.math.ArrayDisplay

overlayLine(int, int, int, int, String) - Method in class woSource.math.ArrayDisplay

overlayLine(int, int, int, int, Color) - Method in class woSource.math.ArrayDisplay

overlayLine(float, float, float, float) - Method in class woSource.math.ArrayDisplay

overlayLine(float, float, float, float, String) - Method in class woSource.math.ArrayDisplay

overlayLine(float, float, float, float, Color) - Method in class woSource.math.ArrayDisplay

overlayLines(Polygon3D, int) - Method in class woSource.math.ArrayDisplay

for connected polygons

overlayLines(Polygon3D, int, String) - Method in class woSource.math.ArrayDisplay

overlayLines(Polygon3D[], int) - Method in class woSource.math.ArrayDisplay

overlayLines(Polygon3D[], int, String) - Method in class woSource.math.ArrayDisplay

overlayLines(Polygon2D, int) - Method in class woSource.math.ArrayDisplay

draws connected lines (e.g.

overlayLines(Polygon2D, int, String) - Method in class woSource.math.ArrayDisplay

overlayLines(Polygon2D[], int) - Method in class woSource.math.ArrayDisplay

overlayLines(Polygon2D[], int, String) - Method in class woSource.math.ArrayDisplay

overlayLines(Point2D[]) - Method in class woSource.math.ArrayDisplay

overlayLines(Point2D[], String) - Method in class woSource.math.ArrayDisplay

overlayLines(Point2D[], boolean) - Method in class woSource.math.ArrayDisplay

overlayLines(Point2D[], boolean, String) - Method in class woSource.math.ArrayDisplay

overlayLines(float[][], boolean) - Method in class woSource.math.ArrayDisplay

overlayLines(float[][], String) - Method in class woSource.math.ArrayDisplay

overlayLines(float[][], boolean, String) - Method in class woSource.math.ArrayDisplay

overlayLines(float[][], int, boolean, String) - Method in class woSource.math.ArrayDisplay

overlayPoint(Point2D, int) - Method in class woSource.math.ArrayDisplay

overlayPoint(Point2D, int, String) - Method in class woSource.math.ArrayDisplay

overlayPoint(float, float, int) - Method in class woSource.math.ArrayDisplay

overlayPoint(float, float, int, String) - Method in class woSource.math.ArrayDisplay

assumes that the x,y passed in means center of mark

overlayPoints(Polygon3D, int) - Method in class woSource.math.ArrayDisplay

WO 9/22/10 3D points to accept polygons that may jump to another slice, but here only want to show points on the current slice.

overlayPoints(Polygon3D, int, String) - Method in class woSource.math.ArrayDisplay

overlayPoints(Polygon3D[], int) - Method in class woSource.math.ArrayDisplay

overlayPoints(Polygon3D[], int, String) - Method in class woSource.math.ArrayDisplay

overlayPoints(Polygon2D, int) - Method in class woSource.math.ArrayDisplay

overlayPoints(Polygon2D, int, String) - Method in class woSource.math.ArrayDisplay

overlayPoints(Polygon2D[], int) - Method in class woSource.math.ArrayDisplay

overlayPoints(Polygon2D[], int, String) - Method in class woSource.math.ArrayDisplay

overlayPoints(Point2D[], int) - Method in class woSource.math.ArrayDisplay

overlayPoints(Point2D[], int, String) - Method in class woSource.math.ArrayDisplay

overlayPoints(Point3D[], int) - Method in class woSource.math.ArrayDisplay

WO created 12/23/2010 assumes each 3D point can be anywhere

overlayPoints(Point3D[], int, String) - Method in class woSource.math.ArrayDisplay

overlayPoints(Point3Dint[], int) - Method in class woSource.math.ArrayDisplay

overlayPoints(Point3Dint[], int, String) - Method in class woSource.math.ArrayDisplay

overlayPoints(float[], int) - Method in class woSource.math.ArrayDisplay

overlayPoints(float[], int, String) - Method in class woSource.math.ArrayDisplay

overlayPoints(float[][], int) - Method in class woSource.math.ArrayDisplay

overlayPoints(float[][], int, String) - Method in class woSource.math.ArrayDisplay

overlayPoints(float[][], int, int, String) - Method in class woSource.math.ArrayDisplay

overlayPoints(float[][][], int) - Method in class woSource.math.ArrayDisplay

overlayPoints(float[][][], int, String) - Method in class woSource.math.ArrayDisplay

overlaySmoothedPolygon(Polygon2D, int, String) - Method in class woSource.math.ArrayDisplay

overlayText(String, int, int) - Method in class woSource.math.ArrayDisplay

overlayText(String, int, int, String) - Method in class woSource.math.ArrayDisplay

overlayText(String, float, float) - Method in class woSource.math.ArrayDisplay

overlayText(String, float, float, String) - Method in class woSource.math.ArrayDisplay

overlayVectors(float[][][]) - Method in class woSource.math.ArrayDisplay

plot line vector at each pixel in image.

overlayVectors(float[][][][]) - Method in class woSource.math.ArrayDisplay

P

pad(float[][][], int, int, int) - Static method in class woSource.math.ImgProc

pad array for fourier convolution operation
assume K is a kernel generated from gaussianKernel() or the like where the kernel center is at (kw/2, kh/2, kd/2), and kw,kh,kd are odd-valued in the padded version, the padded kernel is to be stored in 3D wrap-around and K.lengths < A.lengths

paddedFT(short[]) - Static method in class woSource.math.MathII

WO 1/4/11 code to take any sized array, pad it the minimal amount 2^n and run realFT()

paddedFT(short[][]) - Static method in class woSource.math.MathII

paddedFT(short[][][]) - Static method in class woSource.math.MathII

paddedFT(float[]) - Static method in class woSource.math.MathII

paddedFT(float[][]) - Static method in class woSource.math.MathII

paddedFT(float[][][]) - Static method in class woSource.math.MathII

paddedFT(short[][], int, int) - Static method in class woSource.math.MathII

versions that permit specifying the padding size (i.e.

paddedFT(short[][][], int, int, int) - Static method in class woSource.math.MathII

paddedFT(float[][], int, int) - Static method in class woSource.math.MathII

paddedFT(float[][][], int, int, int) - Static method in class woSource.math.MathII

padding - Variable in class woSource.math.NoduleCandidate

paintDoubleBuffered(Graphics) - Method in class woSource.ScreenSelectorCanvas

parabolic_interpol(double, double, double, double, double, double, double) - Static method in class woSource.math.MathII

parabolic approximation functions are very useful when trying to zone in on local min/max values
note: some of these use Matrix manipulations obtained from Jama

parabolic_interpol(float, float, float, float, float, float, float) - Static method in class woSource.math.MathII

parabolic_interpol(Point2D, Point2D, double, Point2D, double, Point2D, double) - Static method in class woSource.math.MathII

ones that utilize Point2D values.

parabolic_interpol2D(Matrix, Point2D) - Static method in class woSource.math.MathII

parabolic_minMaxLoc(double, double, double, double, double, double) - Static method in class woSource.math.MathII

min/max occurs at dY/dX = 0 ==> x = -b/2c

parabolic_minMaxLoc(float, float, float, float, float, float) - Static method in class woSource.math.MathII

parabolic_minMaxLoc(Point2D, Point2D, double, Point2D, double, Point2D, double) - Static method in class woSource.math.MathII

parabolic_minMaxSoln2D(Point2D[], int) - Static method in class woSource.math.MathII

WO 11/8/00 2D prabolic interpolation.

parabolic_minMaxVal(double, double, double, double, double, double) - Static method in class woSource.math.MathII

parabolic_minMaxVal(float, float, float, float, float, float) - Static method in class woSource.math.MathII

parabolic_minMaxVal(Point2D, double, Point2D, double, Point2D, double) - Static method in class woSource.math.MathII

parClipEndPtIndex - Variable in class woSource.math.VesselBranch

parentIndex - Variable in class woSource.math.VesselBranch

parRadRatioThresh - Variable in class woSource.VesselSegm

parseComplex(String) - Static method in class woSource.math.Complex

parThetaOffset - Variable in class woSource.math.VesselBranch

patientDir - Variable in class woSource.HeartSegm

patientID - Variable in class woSource.math.LIDCnodule

patientID - Variable in class woSource.math.NoduleCandidate

patientOutputDir - Variable in class woSource.HeartSegm

PetCTregistration - Class in woSource

PetCTregistration() - Constructor for class woSource.PetCTregistration

PI - Static variable in class woSource.math.ArraysI

pi - Static variable in class woSource.math.ArraysI

pi() - Static method in class woSource.math.Complex

PI - Variable in class woSource.math.HeartLongAxis

PI - Static variable in class woSource.math.MathI

PI - Static variable in class woSource.math.MathII

pixelEndoLambdas - Variable in class woSource.ImageRegistrationPS

pixelEndoVolumes - Variable in class woSource.ImageRegistrationPS

plane_sep(float[], float[], float[], float[]) - Static method in class woSource.math.MathII

sep between the plane defined by the 3 points and the test point (positive number)

plane_sep(Point3D, float[], float[], float[]) - Static method in class woSource.math.MathII

plugMaskAtPoint(int, int) - Method in class woSource.math.VesselTree

1/8/2012 intent is to void pixels in the mask image to block the mask at branch point brPtIndex.

plus(float[][][], float[][][]) - Static method in class woSource.math.ArraysI

resultant array is element-wise addition of A's and B's elements

plus(float[][][], float) - Static method in class woSource.math.ArraysI

plus(byte[][][], byte[][][]) - Static method in class woSource.math.ArraysI

plus(byte[][][], int) - Static method in class woSource.math.ArraysI

plus(short[][][], int) - Static method in class woSource.math.ArraysI

plus(short[][], short[][]) - Static method in class woSource.math.ArraysI

plus(int[][], int[][]) - Static method in class woSource.math.ArraysI

plus(float[][], float[][]) - Static method in class woSource.math.ArraysI

plus(Complex, Complex) - Static method in class woSource.math.Complex

plus(Complex, double) - Static method in class woSource.math.Complex

plus(double, Complex) - Static method in class woSource.math.Complex

plus(double, double) - Static method in class woSource.math.Complex

plus(Complex) - Method in class woSource.math.Complex

plus(double) - Method in class woSource.math.Complex

plusEquals(Complex) - Method in class woSource.math.Complex

plusEquals(double) - Method in class woSource.math.Complex

plusInfinity() - Static method in class woSource.math.Complex

plusJay() - Static method in class woSource.math.Complex

plusOne() - Static method in class woSource.math.Complex

Point2D - Class in woSource.math

Point2D() - Constructor for class woSource.math.Point2D

Point2D(Point2D) - Constructor for class woSource.math.Point2D

Point2D(float, float, float) - Constructor for class woSource.math.Point2D

Point3D - Class in woSource.math

Point3D() - Constructor for class woSource.math.Point3D

Point3D(float, float, float, float) - Constructor for class woSource.math.Point3D

Point3D(Point3D) - Constructor for class woSource.math.Point3D

Point3Dint - Class in woSource.math

Point3Dint() - Constructor for class woSource.math.Point3Dint

Point3Dint(Point3Dint) - Constructor for class woSource.math.Point3Dint

Point3Dint(int, int, int, float) - Constructor for class woSource.math.Point3Dint

Point3Dviewer - Class in woSource

WO 9/5/2014 implements a user-interactive viewer for 3D points.

Point3Dviewer() - Constructor for class woSource.Point3Dviewer

Point3Dviewer(float[][]) - Constructor for class woSource.Point3Dviewer

Point3Dviewer(float[][][]) - Constructor for class woSource.Point3Dviewer

Point3Dviewer(float[][][][]) - Constructor for class woSource.Point3Dviewer

Point3Dviewer(float[][][][][][]) - Constructor for class woSource.Point3Dviewer

Point3Dviewer(HeartSegm) - Constructor for class woSource.Point3Dviewer

Point3Dviewer.Updater - Class in woSource

Point4D - Class in woSource.math

Point4D() - Constructor for class woSource.math.Point4D

Point4D(float, float, float, float, String, float) - Constructor for class woSource.math.Point4D

Point4D(Point3D, float, String) - Constructor for class woSource.math.Point4D

Point4D(float, float, float, float, float) - Constructor for class woSource.math.Point4D

Point4D(Point3D) - Constructor for class woSource.math.Point4D

Point4D(Point4D) - Constructor for class woSource.math.Point4D

Point4Dint - Class in woSource.math

Point4Dint() - Constructor for class woSource.math.Point4Dint

Point4Dint(int, int, int, int, String, float) - Constructor for class woSource.math.Point4Dint

Point4Dint(Point3Dint, int, String) - Constructor for class woSource.math.Point4Dint

Point4Dint(int, int, int, int, float) - Constructor for class woSource.math.Point4Dint

Point4Dint(Point3Dint) - Constructor for class woSource.math.Point4Dint

Point4Dint(Point4Dint) - Constructor for class woSource.math.Point4Dint

Point_sep(Point2D, Point2D) - Static method in class woSource.math.MathII

Point_sep(Point3D, Point3D) - Static method in class woSource.math.MathII

pointDisplaySize - Variable in class woSource.Point3Dviewer

points - Variable in class woSource.InteractiveSnake.Snake

polar(double, double) - Method in class woSource.math.Complex

polarDeg(double, double) - Method in class woSource.math.Complex

polarRad(double, double) - Method in class woSource.math.Complex

Polygon2D - Class in woSource.math

polygon with coords as float WO 12/17/01

Polygon2D() - Constructor for class woSource.math.Polygon2D

Polygon2D(float[], float[]) - Constructor for class woSource.math.Polygon2D

Polygon2D(float[], float[], int) - Constructor for class woSource.math.Polygon2D

Polygon2D(Point2D[]) - Constructor for class woSource.math.Polygon2D

Polygon2D(Point2D[], int) - Constructor for class woSource.math.Polygon2D

Polygon2D(Point2D[], int, int) - Constructor for class woSource.math.Polygon2D

Polygon3D - Class in woSource.math

Polygon3D() - Constructor for class woSource.math.Polygon3D

Polygon3D(float[], float[], float[]) - Constructor for class woSource.math.Polygon3D

Polygon3D(float[], float[], float[], int) - Constructor for class woSource.math.Polygon3D

Polygon3D(Point3D[]) - Constructor for class woSource.math.Polygon3D

Polygon3D(Point3D[], int) - Constructor for class woSource.math.Polygon3D

Polygon3D(Point3D[], int, int) - Constructor for class woSource.math.Polygon3D

Polygon3Dint - Class in woSource.math

Polygon3Dint() - Constructor for class woSource.math.Polygon3Dint

Polygon3Dint(int[], int[], int[]) - Constructor for class woSource.math.Polygon3Dint

Polygon3Dint(int[], int[], int[], int) - Constructor for class woSource.math.Polygon3Dint

population(int, int, int, int) - Method in class woSource.DTIanalysis

populationBasis(int, int, int[]) - Method in class woSource.DTIanalysis

function ret=populationBasis(i,order,c) if order==0 ret=c; else j=mod(i,3); c(j+1)=c(j+1)+1; ret=populationBasis((i-j)/3,order-1,c); end

pow(Complex) - Method in class woSource.math.Complex

pow(Complex, Complex) - Static method in class woSource.math.Complex

pow(double) - Method in class woSource.math.Complex

pow(Complex, double) - Static method in class woSource.math.Complex

pow(int) - Method in class woSource.math.Complex

pow(Complex, int) - Static method in class woSource.math.Complex

pow(double, Complex) - Static method in class woSource.math.Complex

pow(int, int) - Static method in class woSource.math.MathI

pow(float, float) - Static method in class woSource.math.MathI

pow(float, int) - Static method in class woSource.math.MathI

pow(double, int) - Static method in class woSource.math.MathI

pow(double, double) - Static method in class woSource.math.MathI

PowerSpectrum1D(float[], float[]) - Static method in class woSource.math.MathII

perform one-sided power spectral density
for power spectrum use compilation of '+' and '-' frequences and real and imaginary parts, where present
note: NumRec puts real of k=0 into slot [0] & real of k=N/2 into slot [1]
the rest go as: real of k=1 goes into slot[2], img k=1 goes into [3]
also: for real vals freq[-k] == freq[k]^* (complex conjugate) and not kept
see Num Rec section 13.4 (p551) and 12.0

PowerSpectrum2D(float[][], float[][]) - Static method in class woSource.math.MathII

PowerSpectrum3D(float[][][], float[][][]) - Static method in class woSource.math.MathII

prepgd - Variable in class woSource.noduleDetectionModule

preProcessDiffImages() - Method in class woSource.DTIanalysis

print(float[][][]) - Static method in class woSource.math.ArraysI

my ArraysDisplay 3D conventions [depth][width][height]

print(float[][][], String) - Static method in class woSource.math.ArraysI

print(float[][][], int, int, int, String) - Static method in class woSource.math.ArraysI

print(float[][], int, int, String) - Static method in class woSource.math.ArraysI

print(float[][], int, int) - Static method in class woSource.math.ArraysI

print(float[][]) - Static method in class woSource.math.ArraysI

print(float[][], String) - Static method in class woSource.math.ArraysI

print(float[], int, String) - Static method in class woSource.math.ArraysI

print(float[], int) - Static method in class woSource.math.ArraysI

print(float[], String) - Static method in class woSource.math.ArraysI

print(float[]) - Static method in class woSource.math.ArraysI

print(double[][], int, int, String) - Static method in class woSource.math.ArraysI

print(double[][], int, int) - Static method in class woSource.math.ArraysI

print(double[][]) - Static method in class woSource.math.ArraysI

print(double[][], String) - Static method in class woSource.math.ArraysI

print(double[], int, String) - Static method in class woSource.math.ArraysI

print(double[], int) - Static method in class woSource.math.ArraysI

print(double[], String) - Static method in class woSource.math.ArraysI

print(double[]) - Static method in class woSource.math.ArraysI

print(int[][], int, int, String) - Static method in class woSource.math.ArraysI

print(int[][], int, int) - Static method in class woSource.math.ArraysI

print(int[][]) - Static method in class woSource.math.ArraysI

print(int[][], String) - Static method in class woSource.math.ArraysI

print(int[], int, String) - Static method in class woSource.math.ArraysI

print(int[], int) - Static method in class woSource.math.ArraysI

print(int[], String) - Static method in class woSource.math.ArraysI

print(short[]) - Static method in class woSource.math.ArraysI

print(short[], int) - Static method in class woSource.math.ArraysI

print(short[], int, String) - Static method in class woSource.math.ArraysI

print(byte[], int, String) - Static method in class woSource.math.ArraysI

print(byte[], int) - Static method in class woSource.math.ArraysI

print(byte[], String) - Static method in class woSource.math.ArraysI

print(byte[]) - Static method in class woSource.math.ArraysI

print(boolean[], int, String) - Static method in class woSource.math.ArraysI

print(boolean[], int) - Static method in class woSource.math.ArraysI

print(boolean[], String) - Static method in class woSource.math.ArraysI

print(boolean[]) - Static method in class woSource.math.ArraysI

print(boolean[][], int, int, String) - Static method in class woSource.math.ArraysI

print(boolean[][], int, int) - Static method in class woSource.math.ArraysI

print(boolean[][]) - Static method in class woSource.math.ArraysI

print(boolean[][], String) - Static method in class woSource.math.ArraysI

print(String[], int, String) - Static method in class woSource.math.ArraysI

print(String[], int) - Static method in class woSource.math.ArraysI

print(String[], String) - Static method in class woSource.math.ArraysI

print(String[]) - Static method in class woSource.math.ArraysI

print(String[][], String) - Static method in class woSource.math.ArraysI

print(String[][], int, int, String) - Static method in class woSource.math.ArraysI

print(Point2D[], String) - Static method in class woSource.math.ArraysI

print(Point2D[], int, String) - Static method in class woSource.math.ArraysI

print(Point3D[], String) - Static method in class woSource.math.ArraysI

print(Point3D[], int, String) - Static method in class woSource.math.ArraysI

print(Point3Dint[], String) - Static method in class woSource.math.ArraysI

print(Point3Dint[], int, String) - Static method in class woSource.math.ArraysI

print(Point4D[], String) - Static method in class woSource.math.ArraysI

print(Point4D[], int, String) - Static method in class woSource.math.ArraysI

print(LIDCnodule[], String) - Static method in class woSource.math.ArraysI

print(LIDCnodule[], int, String) - Static method in class woSource.math.ArraysI

print(LIDCnodule[][], String) - Static method in class woSource.math.ArraysI

2/21/11 this version permits different size of 2nd dimension for each 1st dim

print(NoduleCandidate[], String) - Static method in class woSource.math.ArraysI

print(NoduleCandidate[], int, String) - Static method in class woSource.math.ArraysI

print(NoduleCandidate[][], String) - Static method in class woSource.math.ArraysI

print(String) - Method in class woSource.math.Complex

print() - Method in class woSource.math.Complex

print(String, Complex[]) - Static method in class woSource.math.Complex

print(Complex[]) - Static method in class woSource.math.Complex

println(String) - Method in class woSource.math.Complex

println() - Method in class woSource.math.Complex

println(String, Complex[]) - Static method in class woSource.math.Complex

println(Complex[]) - Static method in class woSource.math.Complex

printNodalParams() - Method in class woSource.math.VesselBranch

intended to printout to file the fitted nodal values and radius that describes the model of the branch

PrintSimTreeParams() - Method in class woSource.math.VesselTree

printTreeHierarchy() - Method in class woSource.math.VesselTree

ProhibitInwardPoints - Variable in class woSource.InteractiveSnake

prosph2cart(float, float, float) - Method in class woSource.math.HeartLongAxis

prosph2cart(float[]) - Method in class woSource.math.HeartLongAxis

prosph2cart(double[]) - Method in class woSource.math.HeartLongAxis

prosph2cart(double, double, double) - Method in class woSource.math.HeartLongAxis

prosph2cart(float, float, float, float) - Static method in class woSource.math.MathII

prosph2cart(float[], float) - Static method in class woSource.math.MathII

prosph2cart(double[], double) - Static method in class woSource.math.MathII

prosph2cart(double, double, double, double) - Static method in class woSource.math.MathII

PScoeffsToString() - Method in class woSource.ImageRegistrationPS

PSfitOrder - Variable in class woSource.HeartSegm

pt - Variable in class woSource.InteractiveSnake.Candidates

Pt1 - Variable in class woSource.math.HyperSkelPair

Pt2 - Variable in class woSource.math.HyperSkelPair

pt_external_energy(int) - Method in class woSource.InteractiveSnake.Snake

pt_internal_energy(int, Point2D) - Method in class woSource.InteractiveSnake.Snake

ptAtLVapex - Variable in class woSource.math.HeartLongAxis

ptAtMVcentroid - Variable in class woSource.math.HeartLongAxis

ptEdgeFound - Variable in class woSource.InteractiveSnake.Snake

PTLAmasksWereReadIn - Variable in class woSource.PulmonaryTrunkSegm

pts - Variable in class woSource.math.VesselBranch

ptSeedx - Variable in class woSource.PulmonaryTrunkSegm

ptSeedy - Variable in class woSource.PulmonaryTrunkSegm

ptSeedz - Variable in class woSource.PulmonaryTrunkSegm

ptviewer - Variable in class woSource.HeartSegm

PulmonaryTrunkSegm - Class in woSource

PulmonaryTrunkSegm by W.

PulmonaryTrunkSegm() - Constructor for class woSource.PulmonaryTrunkSegm

pulmTrunkMask - Variable in class woSource.humanLungSegm

pulmTrunkMask - Variable in class woSource.VesselSegm

putAmoebaCurValues(float[]) - Method in class woSource.ImageRegistration

PYTHAG(double, double) - Static method in class woSource.math.OptMath

R

radius - Variable in class woSource.math.NoduleCandidate

RatImageAdjuster - Class in woSource

RatImageAdjuster by W.

RatImageAdjuster() - Constructor for class woSource.RatImageAdjuster

Read(String) - Method in class woSource.DoseReader

Read(String) - Method in class woSource.DoseReader_Oct2012_oldUR

read() - Method in class woSource.ImageRegistration

read(String, int) - Method in class woSource.ImageRegistrationPS

Read() - Method in class woSource.InteractiveSnake.Snake

read(byte[][][], String) - Static method in class woSource.math.ArraysI

read(int[], String) - Static method in class woSource.math.ArraysI

read(int[][], String) - Static method in class woSource.math.ArraysI

read(String) - Static method in class woSource.math.ArraysI

read(float[], String) - Static method in class woSource.math.ArraysI

read(float[][], String) - Static method in class woSource.math.ArraysI

read(float[][][], String) - Static method in class woSource.math.ArraysI

read(float[][][][], String) - Static method in class woSource.math.ArraysI

read(float[][][][][], String) - Static method in class woSource.math.ArraysI

read(double[], String) - Static method in class woSource.math.ArraysI

read(double[][], String) - Static method in class woSource.math.ArraysI

read(Point3D[], String) - Static method in class woSource.math.ArraysI

read(Point3D[], String, boolean) - Static method in class woSource.math.ArraysI

read(Point4D[], String) - Static method in class woSource.math.ArraysI

read(Point4D[], String, boolean) - Static method in class woSource.math.ArraysI

read(Polygon2D, String) - Static method in class woSource.math.ArraysI

read(Polygon2D[], String) - Static method in class woSource.math.ArraysI

read(Polygon3D[], String) - Static method in class woSource.math.ArraysI

read(Polygon3Dint[], String) - Static method in class woSource.math.ArraysI

read(LIDCnodule[], String) - Static method in class woSource.math.ArraysI

read(LIDCnodule[][], String) - Static method in class woSource.math.ArraysI

read(NoduleCandidate[], String) - Static method in class woSource.math.ArraysI

read(String) - Method in class woSource.math.Rectangle3D

Read(String) - Method in class woSource.SnakeReader

read_sparse(float[][][][], String) - Static method in class woSource.math.ArraysI

read_sparse(float[][][][][], String) - Static method in class woSource.math.ArraysI

ReadASnakeFile(String) - Method in class woSource.DVHCalc

ReadASnakeFile(String) - Method in class woSource.SnakeReader

readComplex(String) - Static method in class woSource.math.Complex

readComplex(String, String) - Static method in class woSource.math.Complex

readComplex(String, Complex) - Static method in class woSource.math.Complex

readComplex() - Static method in class woSource.math.Complex

readDiffImages() - Method in class woSource.DTIanalysis

readerID - Variable in class woSource.math.LIDCnodule

ReadFirstSliceInfo() - Method in class woSource.DVHCalc

readIn_allImages() - Method in class woSource.HeartSegm

readInAirwayMaskFiles() - Method in class woSource.AirwaySegm

readInAllHeartLAinfo() - Method in class woSource.HeartSegm

readInAllImagesAtTime(int) - Method in class woSource.HeartSegm

readInDoseProfile(String) - Method in class woSource.DoseCalc

readInfo(String) - Method in class woSource.math.HeartLongAxis

readInfo(String) - Method in class woSource.math.SimTagImageInfo

readInImageFile(byte[][], String) - Static method in class woSource.math.ImgProc

readInImageFile(short[][], String) - Static method in class woSource.math.ImgProc

readInImageFiles(byte[][][], String, String[], String) - Static method in class woSource.math.ImgProc

readInImageFiles(short[][][], String, String[], String) - Static method in class woSource.math.ImgProc

readInImageFiles(float[][][], String, String[], String) - Static method in class woSource.math.ImgProc

readInLIDCdata() - Method in class woSource.LIDCtruthOpt

readInMaskFiles(String, String[], String) - Static method in class woSource.math.ImgProc

readInOrComputeAirwayMask() - Method in class woSource.VesselSegm

readInOrComputeConnTissMask() - Method in class woSource.VesselSegm

readInOrComputeLungVolMask() - Method in class woSource.PulmonaryTrunkSegm

readInOrComputeLungVolMask() - Method in class woSource.VesselSegm

readInOrComputePTLAmasks() - Method in class woSource.VesselSegm

readInPTLAmasks() - Method in class woSource.VesselSegm

readInQueryImageFiles(byte[][][], String, String) - Static method in class woSource.math.ImgProc

readInQueryImageFiles(byte[][][], String, String[], String) - Static method in class woSource.math.ImgProc

readInQueryImageFiles(short[][][], String, String) - Static method in class woSource.math.ImgProc

readInQueryImageFiles(short[][][], String, String[], String) - Static method in class woSource.math.ImgProc

readInQueryImageFiles(float[][][], String, String) - Static method in class woSource.math.ImgProc

readInQueryImageFiles(float[][][], String, String[], String) - Static method in class woSource.math.ImgProc

readInQueryMaskFiles(String, String[], String) - Static method in class woSource.math.ImgProc

readNodalParams(BufferedReader) - Method in class woSource.math.VesselBranch

intended to read in the lines of code (created above) from the openned file r and set the branch params to match

readParams() - Method in class woSource.HistoHisto_reg

readPTdata(String) - Method in class woSource.PulmonaryTrunkSegm

ReadSimTreeParams(String) - Method in class woSource.math.VesselTree

ReadSimTreeParams(String) - Method in class woSource.VesselSegm

ReadSnakeFiles() - Method in class woSource.DVHCalc

readStudyInfo() - Method in class woSource.HeartSegm

readT1s() - Method in class woSource.DTIanalysis

realFt(float[]) - Static method in class woSource.math.MathII

WO 1/4/11 this version to return in same complex number format as 2D and 3D versions

realFt(float[][]) - Static method in class woSource.math.MathII

WO 7/2/01 my 2D to 3D driver.

realFt(float[][][]) - Static method in class woSource.math.MathII

3D FT and InverseFT.

realFt(byte[][][]) - Static method in class woSource.math.MathII

realFt(short[][][]) - Static method in class woSource.math.MathII

realFt(int[][][]) - Static method in class woSource.math.MathII

realFt1D(float[], float[], float[]) - Static method in class woSource.math.MathII

WO these are my functions to run the Numerical Recipe fourier functions
my take in the data[0..N-1] and empty real[0..N/2+1] and im[] arrays
on output, I fill the fourier tranform arrays.

realFt1D(float[], int, float[], float[]) - Static method in class woSource.math.MathII

realInvFt(float[][]) - Static method in class woSource.math.MathII

realInvFt(float[][][]) - Static method in class woSource.math.MathII

realInvFt1D(float[], float[], float[]) - Static method in class woSource.math.MathII

realInvFt1D(float[], float[], float[], int) - Static method in class woSource.math.MathII

reallocateLoopedBranchesChildren(int) - Method in class woSource.VesselSegm

reallocate branch points and children from loopedFrom side to loopedTo side.

reallocateLoopLoc(int) - Method in class woSource.VesselSegm

goal is to reallocate the points on the fromBr onto the To branch, then redefine the loopLoc pair
uses int[][] loopLocs[nLoopPts][4] = [looped-to br, looped-to tree, looped-from br, looped-from tree].

recolorize(ImagePlus, int[], String[]) - Method in class woSource.HistoBinAdjuster

reCreateSimImage() - Method in class woSource.math.VesselTree

Rectangle3D - Class in woSource.math

Rectangle3D() - Constructor for class woSource.math.Rectangle3D

Rectangle3D(int, int, int, int, int, int) - Constructor for class woSource.math.Rectangle3D

Rectangle3D(Rectangle3D) - Constructor for class woSource.math.Rectangle3D

redimension(short[][]) - Static method in class woSource.math.ArraysI

convert from 2D array into one long 1D array using convensions in imageProcessor

redisplay() - Method in class woSource.CellMigration

redisplay() - Method in class woSource.HistoBinAdjuster

redisplay() - Method in class woSource.humanLungSegm

redisplay() - Method in class woSource.ImageReviewer

redisplay() - Method in class woSource.LIDCreview

redisplay() - Method in class woSource.MIPSviewer

redisplay() - Method in class woSource.MIPSviewerColor

redisplay() - Method in class woSource.noduleDetection

redisplay() - Method in class woSource.noduleDetectionModule

reFillMasks(int) - Method in class woSource.PulmonaryTrunkSegm

refresh() - Method in class woSource.math.ArrayDisplay

refreshGD() - Method in class woSource.Point3Dviewer

refreshImage() - Method in class woSource.math.ArrayDisplay

refresh via the canvas is less brutal that window.updateAndDraw() so is the preferred way to clear the screen.

refreshScreen() - Method in class woSource.HeartSegm

refreshScreen() - Method in class woSource.InteractiveSnake

refVoxelLocs - Variable in class woSource.math.SeriesImagesClass

reg2DoseVolume() - Method in class woSource.DoseVsIntensity

RegisterSnake - Class in woSource

RegisterSnake() - Constructor for class woSource.RegisterSnake

registerT1toT2() - Method in class woSource.DTIanalysis

ReInit(InteractiveSnake.Snake) - Method in class woSource.InteractiveSnake.Snake

reInit(int) - Method in class woSource.InteractiveSnake.SnakeStack

relativeWallBrightness - Variable in class woSource.math.VesselBranch

relativeWallThickness - Variable in class woSource.math.VesselBranch

rem(int, int) - Static method in class woSource.math.MathI

remove(boolean[], int) - Static method in class woSource.math.ArraysI

remove point and shorten array

remove(boolean[][], int) - Static method in class woSource.math.ArraysI

remove(int[][], int) - Static method in class woSource.math.ArraysI

remove(float[], int) - Static method in class woSource.math.ArraysI

remove(float[][], int) - Static method in class woSource.math.ArraysI

remove(float[][][], int) - Static method in class woSource.math.ArraysI

remove(String[], int) - Static method in class woSource.math.ArraysI

remove(Point2D[], int) - Static method in class woSource.math.ArraysI

remove(Point3D[], int) - Static method in class woSource.math.ArraysI

remove(Point3Dint[], int) - Static method in class woSource.math.ArraysI

remove(Point4D[], int) - Static method in class woSource.math.ArraysI

remove(NoduleCandidate[], int) - Static method in class woSource.math.ArraysI

removeMaskHoles(boolean[][][]) - Static method in class woSource.math.ImgProc

WO 12/21/2014 clean up mask to remove internal holes and edge noise.

RemovePretzelPts() - Method in class woSource.InteractiveSnake.Snake

removePt(int) - Method in class woSource.InteractiveSnake.Snake

returns true if point removed

removePt(int) - Method in class woSource.InteractiveSnake.SnakeStack

removeSnakePt(InteractiveSnake.Snake, int) - Method in class woSource.lungSnake

removeSnakePt(InteractiveSnake.Snake, int) - Method in class woSource.noduleDetection.lungSnake

renameFilesBatch - Class in woSource

9/4/2013 a batch file renaming program

renameFilesBatch() - Constructor for class woSource.renameFilesBatch

renameFilesBatch() - Method in class woSource.renameFilesBatch

reorderSlices(ImagePlus, int[], int) - Static method in class woSource.math.ImgProc

WO 2/9/11 intent is to reorder slices by the ordered indices gained above

reorderSlices(ImagePlus, String[], int) - Static method in class woSource.math.ImgProc

WO 2/7/2013 apparently I started coding this but never finished.

repairBranchConnection(int, int, int) - Method in class woSource.VesselSegm

repairLoopLoc() identified likely place where the false connection exists, though can be off up/down one level.

repairFalse2DConnection(int, int) - Method in class woSource.VesselSegm

repairFalseLadderConnection(int, int) - Method in class woSource.VesselSegm

repairLoopLocs() - Method in class woSource.VesselSegm

resample_snake(double, int) - Method in class woSource.InteractiveSnake.Snake

reset(double, double) - Method in class woSource.math.Complex

reset() - Method in class woSource.WindowLevelAdjuster

resetALevel(int, int) - Method in class woSource.math.VesselTree

resetLandmark(int, float[]) - Method in class woSource.Point3Dviewer

resetLandmark(int, Point3D) - Method in class woSource.Point3Dviewer

resetLevels() - Method in class woSource.math.VesselTree

resetLUT() - Method in class woSource.HistoBinAdjuster

recalculates the Look Up Table

resetMipRot(float, float) - Static method in class woSource.math.ImgProc

resetView() - Method in class woSource.MIPSviewer

resetView() - Method in class woSource.MIPSviewerColor

resetView() - Method in class woSource.Point3Dviewer

resetwidgets() - Method in class woSource.HeartSegm

resetwidgets() - Method in class woSource.ImageReviewer

resize(short[][], double, double) - Static method in class woSource.math.ArraysI

stretch the image/array

resize(short[][][], double, double, double) - Static method in class woSource.math.ArraysI

resizeHalf(byte[][][]) - Static method in class woSource.math.ArraysI

WO 1/10/2012, ImageJ built-in resize 3D is not doing slice dim correctly.

resizeHalf(short[][][]) - Static method in class woSource.math.ArraysI

resizeHalf(int[][][]) - Static method in class woSource.math.ArraysI

restoreArray(byte[][], Rectangle, Rectangle) - Static method in class woSource.math.ArraysI

restoreArray(byte[][][], Rectangle3D, Rectangle3D) - Static method in class woSource.math.ArraysI

restoreViewer(float[][]) - Method in class woSource.math.HeartLongAxis

resultAd - Variable in class woSource.humanLungSegm

resultAD - Variable in class woSource.ImgRegistration

retrieveAvgRadius() - Method in class woSource.math.VesselBranch

reversePoints() - Method in class woSource.math.VesselBranch

revertToGrayscale(ImagePlus) - Method in class woSource.HistoBinAdjuster

rightLung - Variable in class woSource.humanLungSegm

rmConnTissue() - Method in class woSource.VesselSegm

rmRedundantPts(NoduleCandidate[], float, float) - Method in class woSource.noduleDetection

rmRedundantPts(NoduleCandidate[], float, float, float, float) - Method in class woSource.noduleDetectionModule

roi - Variable in class woSource.InteractiveSnake.Snake

Roi - Variable in class woSource.math.VesselBranch

roiPolygon - Variable in class woSource.InteractiveSnake.Snake

roiRect - Variable in class woSource.InteractiveSnake.Snake

roiRect - Variable in class woSource.math.Image3Dinfo

roiRect - Variable in class woSource.math.SeriesImagesClass

roiType - Variable in class woSource.InteractiveSnake.Snake

ROIwasRead - Variable in class woSource.humanLungSegm

rOrder - Variable in class woSource.DoseReader

rOrder - Variable in class woSource.DoseReader_Oct2012_oldUR

rotateImage(float) - Method in class woSource.math.ArrayDisplay

round(float) - Static method in class woSource.math.MathI

the default (int) function simply truncates any decimal points: (int)(1.9) = 1.

round(double) - Static method in class woSource.math.MathI

run(String) - Method in class woSource.AirwaySegm

run(String, ImagePlus) - Method in class woSource.AirwaySegm

run(String) - Method in class woSource.BeadFinder

run(String) - Method in class woSource.CellMigration

run(String) - Method in class woSource.ColonSegm

run(String, ImagePlus) - Method in class woSource.ColonSegm

run() - Method in class woSource.ContourFit

run(String) - Method in class woSource.ConvertToDicom

run(String) - Method in class woSource.create3DTemplate

run(float, float, float) - Method in class woSource.Deconvolver

run(float, float, float, float) - Method in class woSource.Deconvolver

run(String) - Method in class woSource.Deconvolver

run(String) - Method in class woSource.DicomAnon

run(String) - Method in class woSource.DoseCalc

Constructs an uninitialized ImagePlus.

run(String) - Method in class woSource.DoseReader

run(String) - Method in class woSource.DoseReader_Oct2012_oldUR

run(String) - Method in class woSource.DoseVolumeStats

run(String) - Method in class woSource.DoseVsIntensity

run(String) - Method in class woSource.DTIanalysis

run(String) - Method in class woSource.DVHCalc

run(String) - Method in class woSource.GradientAnalysis3D

run(ImagePlus) - Method in class woSource.HeartSegm

run(String) - Method in class woSource.HeartSegm

run(String, ImagePlus) - Method in class woSource.HeartSegm

run() - Method in class woSource.HistoBinAdjuster

run(String) - Method in class woSource.HistoBinAdjuster

run(String) - Method in class woSource.HistoHisto_reg

run(String) - Method in class woSource.HistoMRreg

run(String) - Method in class woSource.HistoSlideLighting

run(String) - Method in class woSource.humanLungSegm

run(String, ImagePlus) - Method in class woSource.humanLungSegm

run(String) - Method in class woSource.ImageOverlay

run(ArrayColorDisplay) - Method in class woSource.ImageRegistration

run(ArrayColorDisplay3D) - Method in class woSource.ImageRegistration

run(ArrayColorDisplay3D, ArrayColorDisplay) - Method in class woSource.ImageRegistration

run() - Method in class woSource.ImageRegistrationPS

run(float[], float[][], int[]) - Method in class woSource.ImageRegistrationPS

run(String) - Method in class woSource.ImageReviewer

run(String, ImagePlus) - Method in class woSource.ImageReviewer

run(String) - Method in class woSource.ImgRegistration

run(ImagePlus) - Method in class woSource.InteractiveSnake

run(String) - Method in class woSource.InteractiveSnake

run(String, ImagePlus) - Method in class woSource.InteractiveSnake

run(ImageProcessor) - Method in class woSource.InteractiveSnake_Hermite

run(ImageProcessor) - Method in class woSource.InteractiveSnake_Hermite3D

run(String) - Method in class woSource.LesionFinder

run(String) - Method in class woSource.LIDCreview

run(String) - Method in class woSource.LIDCtruthOpt

run() - Method in class woSource.math.ImgProc.ConvolveThread

run() - Method in class woSource.math.ImgProc.CorrCalcThread

run() - Method in class woSource.math.ImgProc.DilateThread

run() - Method in class woSource.math.ImgProc.EdgeFillThread

run() - Method in class woSource.math.ImgProc.ErodeThread

run(boolean[][][]) - Method in class woSource.math.Skeletonize3D

run() - Method in class woSource.math.VesselTree.OptBrNodThread

run() - Method in class woSource.math.VesselTree.OptBrRadThread

run(String) - Method in class woSource.MIPSviewer

run() - Method in class woSource.MIPSviewer.Updater

run(String) - Method in class woSource.MIPSviewerColor

run(String) - Method in class woSource.MotionBlur

run(String) - Method in class woSource.MouseLungSegmentor

run(String) - Method in class woSource.MouseMicroCTlungSegm

run() - Method in class woSource.noduleDetection.myThread

run(String) - Method in class woSource.noduleDetection

run() - Method in class woSource.noduleDetectionModule.myOptThread

run() - Method in class woSource.noduleDetectionModule.NodDetThread

run(String) - Method in class woSource.noduleDetectionModule

run(String, ImagePlus) - Method in class woSource.noduleDetectionModule

run(String) - Method in class woSource.PetCTregistration

run(String) - Method in class woSource.Point3Dviewer

run() - Method in class woSource.Point3Dviewer

run() - Method in class woSource.Point3Dviewer.Updater

run(String) - Method in class woSource.PulmonaryTrunkSegm

run(String, ImagePlus) - Method in class woSource.PulmonaryTrunkSegm

run(String) - Method in class woSource.RatImageAdjuster

run(String, ImagePlus) - Method in class woSource.RatImageAdjuster

run(ImageProcessor) - Method in class woSource.RegisterSnake

run(String) - Method in class woSource.renameFilesBatch

run(String) - Method in class woSource.seededRegionGrowing

run(String) - Method in class woSource.unwrapMR_stack

run(String) - Method in class woSource.VesselSegm

run(String, ImagePlus) - Method in class woSource.VesselSegm

run(String) - Method in class woSource.VisualHumanConvert2Dicom

run(String) - Method in class woSource.VolOverlap

run() - Method in class woSource.WindowLevelAdjuster

run(String) - Method in class woSource.WindowLevelAdjuster

runAsStandAlone - Variable in class woSource.InteractiveSnake

runGui() - Method in class woSource.DicomAnon

runGUI(String) - Method in class woSource.ImageReviewer

runGUI() - Method in class woSource.MIPSviewer

runGUI() - Method in class woSource.Point3Dviewer

runInThread(String) - Method in class woSource.HistoBinAdjuster

runInThread(String) - Method in class woSource.WindowLevelAdjuster

runWalks() - Method in class woSource.CellMigration

RVSeedx - Variable in class woSource.PulmonaryTrunkSegm

RVSeedy - Variable in class woSource.PulmonaryTrunkSegm

RVSeedz - Variable in class woSource.PulmonaryTrunkSegm

S

SAselectedRoi - Variable in class woSource.HeartSegm

saveAsAnimatedGif() - Method in class woSource.math.ArrayDisplay

saveAsAnimatedGif(String) - Method in class woSource.math.ArrayDisplay

saveAsAVI() - Method in class woSource.math.ArrayDisplay

saveAsAVI(String) - Method in class woSource.math.ArrayDisplay

saveAsImage(String) - Method in class woSource.math.ArrayDisplay

This saves only one image, intended for when Depth = 1.

saveAsImage(String, String) - Method in class woSource.math.ArrayDisplay

saveAsImages(String) - Method in class woSource.math.ArrayDisplay

saveAsImages(String, String) - Method in class woSource.math.ArrayDisplay

saveCellPaths() - Method in class woSource.CellMigration

saveConnTissMask - Variable in class woSource.PulmonaryTrunkSegm

saveData() - Method in class woSource.MouseMicroCTlungSegm

saveImage(String) - Method in class woSource.MIPSviewer

saveImage(String) - Method in class woSource.MIPSviewerColor

saveImage(String) - Method in class woSource.Point3Dviewer

SaveMask() - Method in class woSource.InteractiveSnake_Hermite

SaveMask() - Method in class woSource.InteractiveSnake_Hermite3D

SaveMask_asDicom() - Method in class woSource.InteractiveSnake_Hermite

SaveMask_asDicom() - Method in class woSource.InteractiveSnake_Hermite3D

savePTdata() - Method in class woSource.PulmonaryTrunkSegm

saveRVLVmasks - Variable in class woSource.PulmonaryTrunkSegm

saveWindows - Variable in class woSource.InteractiveSnake

scale(byte[][]) - Static method in class woSource.math.ArraysI

change the element values to fit within the given range

scale(byte[][], int, int) - Static method in class woSource.math.ArraysI

scale(byte[][][]) - Static method in class woSource.math.ArraysI

scale(byte[][][], int, int) - Static method in class woSource.math.ArraysI

scale(short[][]) - Static method in class woSource.math.ArraysI

scale(short[][], int, int) - Static method in class woSource.math.ArraysI

scale(short[][][]) - Static method in class woSource.math.ArraysI

scale(short[][][], int, int) - Static method in class woSource.math.ArraysI

scale(int[][]) - Static method in class woSource.math.ArraysI

scale(int[][], int, int) - Static method in class woSource.math.ArraysI

scale(int[][][]) - Static method in class woSource.math.ArraysI

scale(int[][][], int, int) - Static method in class woSource.math.ArraysI

scale(float[][]) - Static method in class woSource.math.ArraysI

scale(float[][], float, float) - Static method in class woSource.math.ArraysI

scale(float[][][]) - Static method in class woSource.math.ArraysI

scale(float[][][], float, float) - Static method in class woSource.math.ArraysI

scale(double[][]) - Static method in class woSource.math.ArraysI

scale(double[][], double, double) - Static method in class woSource.math.ArraysI

scale(double[][][]) - Static method in class woSource.math.ArraysI

scale(double[][][], double, double) - Static method in class woSource.math.ArraysI

scaleKernel(float[][], int, float, float) - Static method in class woSource.math.MathII

scaleROIforDicom() - Method in class woSource.ConvertToDicom

ScreenSelectorCanvas - Class in woSource

WO 3/6/2015 adding FocusListener so that I can keept track of when this window has focus which is useful when have more than 1 SSC window open (e.g.

ScreenSelectorCanvas(ImagePlus) - Constructor for class woSource.ScreenSelectorCanvas

ScreenSelectorCanvas(int, int, ScreenSelectorClass) - Constructor for class woSource.ScreenSelectorCanvas

ScreenSelectorCanvas(ImagePlus, ScreenSelectorClass) - Constructor for class woSource.ScreenSelectorCanvas

ScreenSelectorClass - Class in woSource

ScreenSelectorClass() - Constructor for class woSource.ScreenSelectorClass

search_1D_min(float[], float) - Static method in class woSource.math.OptMath

search_1D_min(float[], float, int) - Static method in class woSource.math.OptMath

sec() - Method in class woSource.math.Complex

sec(Complex) - Static method in class woSource.math.Complex

sech() - Method in class woSource.math.Complex

sech(Complex) - Static method in class woSource.math.Complex

sech(double) - Static method in class woSource.math.MathI

Hyperbolic secant of a double number

seededRegionGrowing - Class in woSource

seededRegionGrowing() - Constructor for class woSource.seededRegionGrowing

seedVoxelValue - Variable in class woSource.PulmonaryTrunkSegm

seedVoxelValue - Variable in class woSource.VesselSegm

seedx - Variable in class woSource.VesselSegm

seedy - Variable in class woSource.VesselSegm

seedz - Variable in class woSource.VesselSegm

segBrain() - Method in class woSource.DTIanalysis

segTumor() - Method in class woSource.DTIanalysis

selfClipEndPtIndex - Variable in class woSource.math.VesselBranch

selfClipFrontPtIndex - Variable in class woSource.math.VesselBranch

sep(LIDCnodule) - Method in class woSource.math.LIDCnodule

sep(float[], Point2D) - Static method in class woSource.math.MathII

sep(Point, Point) - Static method in class woSource.math.MathII

sep(Point2D, Point2D) - Static method in class woSource.math.MathII

sep(Point2D, float[]) - Static method in class woSource.math.MathII

sep(Point3D, float[]) - Static method in class woSource.math.MathII

sep(float[], Point3D) - Static method in class woSource.math.MathII

sep(int[], int[]) - Static method in class woSource.math.MathII

Eucledian distance between 2 points.

sep(float[], float[]) - Static method in class woSource.math.MathII

sep(double[], double[]) - Static method in class woSource.math.MathII

sep(Point2D) - Method in class woSource.math.Point2D

sep(Point3D) - Method in class woSource.math.Point3D

sep(Point3Dint) - Method in class woSource.math.Point3Dint

sep(Point3D) - Method in class woSource.math.Point4D

sep(Point4D) - Method in class woSource.math.Point4D

sep(Point3Dint) - Method in class woSource.math.Point4Dint

sep(Point4Dint) - Method in class woSource.math.Point4Dint

sepByDistAllMasks() - Method in class woSource.PulmonaryTrunkSegm

sepVec(Point3Dint) - Method in class woSource.math.Point3D

returns the unit vector from 'this' to A

sepVec(Point3Dint) - Method in class woSource.math.Point3Dint

returns the unit vector from 'this' to A

seriesImages - Variable in class woSource.HeartSegm

SeriesImagesClass - Class in woSource.math

SeriesImagesClass(String, short[][][], boolean[][][], Rectangle3D) - Constructor for class woSource.math.SeriesImagesClass

SeriesImagesClass(SeriesImagesClass) - Constructor for class woSource.math.SeriesImagesClass

SeriesNames - Variable in class woSource.HeartSegm

Set(InteractiveSnake.Snake) - Method in class woSource.InteractiveSnake.SmoothSnake

set(float, float, float, float) - Method in class woSource.math.Point3D

setAdMagnification(float) - Method in class woSource.Point3Dviewer

setAdScreenLocation(int, int) - Method in class woSource.Point3Dviewer

setAlpha(float) - Method in class woSource.math.ArrayDisplay

setArray(int[]) - Method in class woSource.math.ArrayPlot

setArray(int[], int) - Method in class woSource.math.ArrayPlot

setArray(int[], int, int, int) - Method in class woSource.math.ArrayPlot

setArray(int[], int[], int, int, int) - Method in class woSource.math.ArrayPlot

setArray(float[]) - Method in class woSource.math.ArrayPlot

setArray(float[], int) - Method in class woSource.math.ArrayPlot

setArray(float[], int, float, float) - Method in class woSource.math.ArrayPlot

setArray(float[], float[], int, float, float) - Method in class woSource.math.ArrayPlot

setBackgroundColor(String) - Method in class woSource.math.ArrayDisplay

setBackgroundColor(Color) - Method in class woSource.math.ArrayDisplay

setBackgroundColor(Color) - Method in class woSource.ScreenSelectorCanvas

setBGSimImage(byte[][][]) - Method in class woSource.math.VesselBranch

setBrBGImages(int, int, int) - Method in class woSource.math.VesselTree

create background images.

setButtonLabel(int, String) - Method in class woSource.GenericRecallableDialog

setColors(byte[][]) - Method in class woSource.math.ArrayColorDisplay

setColors(byte[][][]) - Method in class woSource.math.ArrayColorDisplay

setColors(short[][]) - Method in class woSource.math.ArrayColorDisplay

setColors(short[][][]) - Method in class woSource.math.ArrayColorDisplay

setCurCoeffs(float[], float[][]) - Method in class woSource.ImageRegistrationPS

setCurLevel(float) - Method in class woSource.AutoWindowLevel

setCurrentSlice(int) - Method in class woSource.math.ArrayDisplay

setCurrentSnake(int) - Method in class woSource.InteractiveSnake.SnakeStack

setCurWindow(float) - Method in class woSource.AutoWindowLevel

setFileInfo(FileInfo) - Method in class woSource.math.ArrayDisplay

setFilename_addon(String) - Method in class woSource.InteractiveSnake

setFocalPts(float, float, float, float) - Method in class woSource.math.HeartLongAxis

setFocalPts(float, float, float, float, float, float) - Method in class woSource.math.HeartLongAxis

setFocalPts(Point3D, Point3D) - Method in class woSource.math.HeartLongAxis

setFocusButton(int) - Method in class woSource.GenericRecallableDialog

setFullScreen() - Method in class woSource.math.ArrayDisplay

setGdLocation(int, int) - Method in class woSource.Point3Dviewer

setGradDirs(int, String) - Method in class woSource.DTIanalysis

setGUIWinLevelWidgets() - Method in class woSource.ImageReviewer

setHeartRoi(Rectangle) - Method in class woSource.math.SimTagImageInfo

seti() - Static method in class woSource.math.Complex

setImag(double) - Method in class woSource.math.Complex

setInfoFromString(String) - Method in class woSource.math.HeartLongAxis

setInfOption(boolean) - Static method in class woSource.math.Complex

setInfOption(int) - Static method in class woSource.math.Complex

setInputOutputDirs() - Static method in class woSource.math.MathI

setj() - Static method in class woSource.math.Complex

setLevel(int) - Method in class woSource.math.VesselBranch

setLUTcolor(int, int, String, byte[], byte[], byte[]) - Method in class woSource.HistoBinAdjuster

setLVapex(Point3D) - Method in class woSource.math.HeartLongAxis

setMagnification(double) - Method in class woSource.math.ArrayDisplay

setMidSeptumPt(Point3D) - Method in class woSource.math.HeartLongAxis

setmmPerPixelX(float) - Method in class woSource.math.ArrayDisplay

setmmPerPixelY(float) - Method in class woSource.math.ArrayDisplay

setMVcentroid(Point3D) - Method in class woSource.math.HeartLongAxis

setNewEndoEpi() - Method in class woSource.HeartSegm

setNewSeries() - Method in class woSource.HeartSegm

setNewSlice() - Method in class woSource.HeartSegm

setNewSlice() - Method in class woSource.ImageReviewer

setNewSlice() - Method in class woSource.LIDCreview

setNewStudy() - Method in class woSource.ImageReviewer

setNewStudy() - Method in class woSource.LIDCreview

setNewTime() - Method in class woSource.HeartSegm

setOrthoViews(short[][][]) - Method in class woSource.math.ArrayColorDisplay3D

setParentIndex(int) - Method in class woSource.math.VesselBranch

setPatientID(String) - Method in class woSource.math.LIDCnodule

setPixels(byte[][]) - Method in class woSource.math.ArrayColorDisplay

set using ColorProcessor, not the default shortProcessor as with ArrayDisplay

setPixels(byte[][][]) - Method in class woSource.math.ArrayColorDisplay

setPixels(short[][]) - Method in class woSource.math.ArrayColorDisplay

setPixels(short[][][]) - Method in class woSource.math.ArrayColorDisplay

setPixels(int[][]) - Method in class woSource.math.ArrayColorDisplay

setPixels(int[][][]) - Method in class woSource.math.ArrayColorDisplay

setPixels(float[][]) - Method in class woSource.math.ArrayColorDisplay

setPixels(float[][][]) - Method in class woSource.math.ArrayColorDisplay

setPixels(boolean[][]) - Method in class woSource.math.ArrayDisplay

setPixels(byte[][]) - Method in class woSource.math.ArrayDisplay

setPixels(short[][]) - Method in class woSource.math.ArrayDisplay

setPixels(int[][]) - Method in class woSource.math.ArrayDisplay

setPixels(float[][]) - Method in class woSource.math.ArrayDisplay

setPixels(double[][]) - Method in class woSource.math.ArrayDisplay

setPixels(Point3D[][]) - Method in class woSource.math.ArrayDisplay

setPixels(boolean[][][]) - Method in class woSource.math.ArrayDisplay

setPixels(byte[][][]) - Method in class woSource.math.ArrayDisplay

setPixels(short[][][]) - Method in class woSource.math.ArrayDisplay

setPixels(int[][][]) - Method in class woSource.math.ArrayDisplay

setPixels(float[][][]) - Method in class woSource.math.ArrayDisplay

setPixels(double[][][]) - Method in class woSource.math.ArrayDisplay

setPixels(Point3D[][][]) - Method in class woSource.math.ArrayDisplay

setPoint() - Method in class woSource.math.HeartLongAxis

setPointRadii() - Method in class woSource.VesselSegm

set to match distance map [mm], where the distmap was computed correctly even for sliceCenterSep != mmPerPxelX,Y.

setProperty(int, String, Object) - Method in class woSource.math.ArrayDisplay

setReal(double) - Method in class woSource.math.Complex

setRefVoxelLocs() - Method in class woSource.ImageRegistrationPS

setRegDisplay() - Method in class woSource.HistoMR_registration

setRegDisplay() - Method in class woSource.ImageRegistration

setRGBs(byte[][], byte[][], byte[][]) - Method in class woSource.math.ArrayColorDisplay

setRGBs(byte[][][], byte[][][], byte[][][]) - Method in class woSource.math.ArrayColorDisplay

setRoi(Roi) - Method in class woSource.InteractiveSnake.Snake

setRoi(TruncatedEllipseRoi) - Method in class woSource.InteractiveSnake.Snake

setRoi(Rectangle) - Method in class woSource.InteractiveSnake.Snake

setRoi() - Method in class woSource.InteractiveSnake.Snake

setRoi(Rectangle) - Method in class woSource.math.ArrayDisplay

setRoi(Rectangle3D) - Method in class woSource.math.ArrayDisplay

setRoi(Roi) - Method in class woSource.math.ArrayDisplay

setRoi(OvalRoi) - Method in class woSource.math.ArrayDisplay

setRoi(TruncatedEllipseRoi) - Method in class woSource.math.ArrayDisplay

setRoi(PolygonRoi) - Method in class woSource.math.ArrayDisplay

setRoiFillColor(Color) - Method in class woSource.math.ArrayDisplay

setRoiRect() - Method in class woSource.InteractiveSnake.Snake

setScreenLocation(Point) - Method in class woSource.math.ArrayDisplay

setScreenLocation(int, int) - Method in class woSource.math.ArrayDisplay

setScreenSize(int, int) - Method in class woSource.math.ArrayDisplay

setSelectorClass(ScreenSelectorClass) - Method in class woSource.ScreenSelectorCanvas

setShowLabels(boolean) - Method in class woSource.InteractiveSnake.Snake

setShowLabels(boolean) - Method in class woSource.InteractiveSnake.SnakeStack

setSideViewScreenLocation(int, int) - Method in class woSource.math.ArrayColorDisplay3D

setSliceCenterSep(float) - Method in class woSource.math.ArrayDisplay

setSliceLabel(String, int) - Method in class woSource.math.ArrayDisplay

setSliceLabels(String[]) - Method in class woSource.math.ArrayDisplay

setStringString(String, String, int, String, String) - Static method in class woSource.math.MathII

WO 5/18/09 trying to re-set individual values from a base dicom header, passed as 'target'
if there are multiple values on the same line, separated by some delimiter (eg "\") then need to pass that delimiter even if you want just the first value on that line -- need to know where to stop replacing characters.

setTopViewScreenLocation(int, int) - Method in class woSource.math.ArrayColorDisplay3D

setTreeMask(boolean[][][]) - Method in class woSource.math.VesselTree

setUnitVecs() - Method in class woSource.DTIanalysis

setup(String, ImagePlus) - Method in class woSource.InteractiveSnake_Hermite

setup(String, ImagePlus) - Method in class woSource.InteractiveSnake_Hermite3D

setup(short[][][]) - Method in class woSource.MIPSviewer

setup(short[][][], float) - Method in class woSource.MIPSviewer

setup(short[][][], ImagePlus) - Method in class woSource.MIPSviewer

setup(short[][][], float, ImagePlus) - Method in class woSource.MIPSviewer

setup(short[][][], float, Properties[]) - Method in class woSource.MIPSviewer

setup(short[][][], float, ImagePlus, Properties[]) - Method in class woSource.MIPSviewer

setup(boolean[][][]) - Method in class woSource.MIPSviewer

setup(boolean[][][], float) - Method in class woSource.MIPSviewer

setup(boolean[][][], ImagePlus) - Method in class woSource.MIPSviewer

setup(boolean[][][], float, ImagePlus) - Method in class woSource.MIPSviewer

setup(boolean[][][], float, Properties[]) - Method in class woSource.MIPSviewer

setup(boolean[][][], float, ImagePlus, Properties[]) - Method in class woSource.MIPSviewer

setup(byte[][][]) - Method in class woSource.MIPSviewer

setup(byte[][][], float) - Method in class woSource.MIPSviewer

setup(byte[][][], ImagePlus) - Method in class woSource.MIPSviewer

setup(byte[][][], float, ImagePlus) - Method in class woSource.MIPSviewer

setup(byte[][][], float, Properties[]) - Method in class woSource.MIPSviewer

setup(byte[][][], float, ImagePlus, Properties[]) - Method in class woSource.MIPSviewer

setup(byte[][][], byte[][][]) - Method in class woSource.MIPSviewerColor

setup(byte[][][], byte[][][], float) - Method in class woSource.MIPSviewerColor

setup(byte[][][], byte[][][], float, Properties[]) - Method in class woSource.MIPSviewerColor

setup(byte[][][], byte[][][], ImagePlus) - Method in class woSource.MIPSviewerColor

setup(byte[][][], byte[][][], float, ImagePlus) - Method in class woSource.MIPSviewerColor

setup(byte[][][], byte[][][], Point4Dint[]) - Method in class woSource.MIPSviewerColor

setup(byte[][][], byte[][][], Point4Dint[], float) - Method in class woSource.MIPSviewerColor

setup(byte[][][], byte[][][], Point4Dint[], float, Properties[]) - Method in class woSource.MIPSviewerColor

setup(byte[][][], byte[][][], Point4Dint[], ImagePlus) - Method in class woSource.MIPSviewerColor

setup(byte[][][], byte[][][], Point4Dint[], float, ImagePlus) - Method in class woSource.MIPSviewerColor

setup(byte[][][], byte[][][], Point4Dint[], float, ImagePlus, Properties[]) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][]) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][], float) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][], float, Properties[]) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][], ImagePlus) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][], float, ImagePlus) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][], Point4Dint[]) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][], Point4Dint[], float) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][], Point4Dint[], float, Properties[]) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][], Point4Dint[], ImagePlus) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][], Point4Dint[], float, ImagePlus) - Method in class woSource.MIPSviewerColor

setup(short[][][], byte[][][], Point4Dint[], float, ImagePlus, Properties[]) - Method in class woSource.MIPSviewerColor

setup(HeartSegm) - Method in class woSource.Point3Dviewer

setup(float[][]) - Method in class woSource.Point3Dviewer

setup(float[][][]) - Method in class woSource.Point3Dviewer

setup(float[][][][]) - Method in class woSource.Point3Dviewer

setup(float[][][][][][]) - Method in class woSource.Point3Dviewer

setupImg() - Method in class woSource.ImageReviewer

setupImg(String) - Method in class woSource.ImageReviewer

setupImg(ImagePlus) - Method in class woSource.ImageReviewer

setupImg(String, ImagePlus) - Method in class woSource.ImageReviewer

provides opportunity to pass in the imp rather than reading it in

setupImg() - Method in class woSource.LIDCreview

setupMIPs(byte[][][], byte[][][]) - Method in class woSource.PulmonaryTrunkSegm

setupMIPs(byte[][][]) - Method in class woSource.RatImageAdjuster

setupMIPs(byte[][][], byte[][][]) - Method in class woSource.VesselSegm

setupPropsLabelsEtc(String, String[], int, Properties[], ScreenSelectorClass) - Method in class woSource.math.ArrayDisplay

setupView(ImagePlus, Properties[]) - Method in class woSource.MIPSviewer

setWindowLevel(float, float) - Method in class woSource.math.ArrayDisplay

assumes that newwin and newlevel values are normalized 0..1

setWindowScale() - Method in class woSource.Point3Dviewer

shiftInZ(int) - Method in class woSource.math.VesselBranch

shiftInZ(int) - Method in class woSource.math.VesselTree

shiftup(short[], int) - Static method in class woSource.math.ArraysI

remove point without shortening array

shiftup(short[], int, int) - Static method in class woSource.math.ArraysI

shiftup(short[][], int) - Static method in class woSource.math.ArraysI

shiftup(short[][], int, int) - Static method in class woSource.math.ArraysI

this has unique definition that it shifts entire 2nd dim down along 1st dim

shiftup(int[], int) - Static method in class woSource.math.ArraysI

shiftup(int[], int, int) - Static method in class woSource.math.ArraysI

shiftup(int[][], int) - Static method in class woSource.math.ArraysI

shiftup(int[][], int, int, int) - Static method in class woSource.math.ArraysI

this has unique definition that it shifts entire 2nd dim down along 1st dim

show() - Method in class woSource.math.ArrayDisplay

show() - Method in class woSource.Point3Dviewer

showAbout() - Method in class woSource.CellMigration

showAbout() - Method in class woSource.ConvertToDicom

showAbout() - Method in class woSource.DicomAnon

showAbout() - Method in class woSource.DoseCalc

showAbout() - Method in class woSource.DoseReader

showAbout() - Method in class woSource.DoseReader_Oct2012_oldUR

showAbout() - Method in class woSource.DoseVolumeStats

showAbout() - Method in class woSource.DoseVsIntensity

showAbout() - Method in class woSource.DTIanalysis

showAbout() - Method in class woSource.DVHCalc

showAbout() - Method in class woSource.HeartSegm

showAbout() - Method in class woSource.HistoHisto_reg

showAbout() - Method in class woSource.HistoMR_registration

showAbout() - Method in class woSource.HistoMRreg

showAbout() - Method in class woSource.humanLungSegm

showAbout() - Method in class woSource.ImageOverlay

showAbout() - Method in class woSource.ImageRegistration

showAbout() - Method in class woSource.ImageRegistrationPS

showAbout() - Method in class woSource.ImgRegistration

showAbout() - Method in class woSource.InteractiveSnake

showAbout() - Method in class woSource.InteractiveSnake_Hermite

showAbout() - Method in class woSource.InteractiveSnake_Hermite3D

showAbout() - Method in class woSource.RegisterSnake

showAbout() - Method in class woSource.renameFilesBatch

showAbout() - Method in class woSource.SnakeReader

showAbout() - Method in class woSource.unwrapMR_stack

showAbout() - Method in class woSource.VisualHumanConvert2Dicom

showAllDisplays() - Method in class woSource.PulmonaryTrunkSegm

showBiggestTree() - Method in class woSource.VesselSegm

showCenterlinePts() - Method in class woSource.VesselSegm

showDialog() - Method in class woSource.GenericRecallableDialog

changes from parent showDialog(): remove accept button

showDistAd - Variable in class woSource.VesselSegm

showEdgeImg - Variable in class woSource.InteractiveSnake

showing3D - Variable in class woSource.math.ArrayDisplay

showingTagsVsFilled - Variable in class woSource.HeartSegm

ShowLabels - Variable in class woSource.InteractiveSnake

ShowLabels - Variable in class woSource.InteractiveSnake_Hermite

ShowLabels - Variable in class woSource.InteractiveSnake_Hermite3D

showProfile() - Method in class woSource.DoseCalc

shuffleLoopLocs() - Method in class woSource.VesselSegm

put first loopLoc to last to setup to rerun repairLoopLocs()

SIGN(double, double) - Static method in class woSource.math.OptMath

simTagImage - Variable in class woSource.math.SimTagImageInfo

SimTagImageInfo - Class in woSource.math

SimTagImageInfo(String) - Constructor for class woSource.math.SimTagImageInfo

SimTagImageInfo(SimTagImageInfo) - Constructor for class woSource.math.SimTagImageInfo

SimTagImageInfo(int, int, float, float, float, float) - Constructor for class woSource.math.SimTagImageInfo

SimTagImageInfo(int, int, float, float, float, float, Rectangle) - Constructor for class woSource.math.SimTagImageInfo

simTagInfo - Variable in class woSource.HeartSegm

simTreeImg - Variable in class woSource.math.VesselTree

sin() - Method in class woSource.math.Complex

sin(Complex) - Static method in class woSource.math.Complex

sin(double) - Static method in class woSource.math.MathI

sin(float) - Static method in class woSource.math.MathI

sinh() - Method in class woSource.math.Complex

sinh(Complex) - Static method in class woSource.math.Complex

sinh(double) - Static method in class woSource.math.MathI

Hyperbolic sine of a double number

sinh(float) - Static method in class woSource.math.MathI

skelAd - Variable in class woSource.VesselSegm

skeletonize(byte[][]) - Static method in class woSource.math.ImgProc

2D skeletonize function from BinaryProcessor
WO 7/2/2012 for true 3D use the skeletonize3D.java in WOmath/

Skeletonize3D - Class in woSource.math

Main class.

Skeletonize3D() - Constructor for class woSource.math.Skeletonize3D

skelWasChanged - Variable in class woSource.math.VesselTree

skipPts - Variable in class woSource.ContourFit

slash - Variable in class woSource.ImageRegistrationPS

slash - Variable in class woSource.PulmonaryTrunkSegm

slash - Variable in class woSource.RatImageAdjuster

slash - Variable in class woSource.VesselSegm

sliceCenterSep - Variable in class woSource.math.ArrayDisplay

sliceI - Variable in class woSource.math.NoduleCandidate

sliceIndex - Variable in class woSource.math.LIDCnodule

SliceLabel - Variable in class woSource.math.ArrayDisplay

SliceLabels - Variable in class woSource.math.ArrayDisplay

SliceNames - Variable in class woSource.HeartSegm

sliceprops - Variable in class woSource.math.ArrayDisplay

sliceThickness - Variable in class woSource.DoseReader

sliceZ - Variable in class woSource.math.LIDCnodule

SliderDim - Variable in class woSource.math.ArrayDisplay

smoothDoseValues(int, int) - Method in class woSource.DoseReader

smoothDoseValues(int, int) - Method in class woSource.DoseReader_Oct2012_oldUR

smoothNods_ptSep - Variable in class woSource.lungSnake

smoothPts - Variable in class woSource.math.VesselBranch

SmoothSnake(InteractiveSnake.Snake) - Constructor for class woSource.InteractiveSnake.SmoothSnake

smoothTreeBranches() - Method in class woSource.math.VesselTree

4/2/2013 Intent is to create smooth fits to the branches for future simulated vessel calc.

Snake() - Constructor for class woSource.InteractiveSnake.Snake

Snake(String) - Constructor for class woSource.InteractiveSnake.Snake

Snake(ImagePlus) - Constructor for class woSource.InteractiveSnake.Snake

Snake(ImageProcessor) - Constructor for class woSource.InteractiveSnake.Snake

Snake(ImageProcessor, String, String, Roi) - Constructor for class woSource.InteractiveSnake.Snake

initializes to generic roi.

snakeAd - Variable in class woSource.InteractiveSnake

snakeDebugSlice - Variable in class woSource.lungSnake

snakegd - Variable in class woSource.InteractiveSnake

snakeptviewer - Variable in class woSource.InteractiveSnake

SnakeReader - Class in woSource

SnakeReader(String) - Constructor for class woSource.SnakeReader

snakes - Variable in class woSource.InteractiveSnake.SnakeStack

snakeStack - Variable in class woSource.InteractiveSnake

SnakeStack(ImagePlus) - Constructor for class woSource.InteractiveSnake.SnakeStack

SnakeStack(ArrayDisplay) - Constructor for class woSource.InteractiveSnake.SnakeStack

SnakeStack(int, String[]) - Constructor for class woSource.InteractiveSnake.SnakeStack

SnakeStack(int, String) - Constructor for class woSource.InteractiveSnake.SnakeStack

solveNNLS(Matrix, float[]) - Static method in class woSource.NNLSSolver

Whee!!! This is my own Java implementation of the NNLS algorithm as described in: Lawson and Hanson, "Solving Least Squares Problems", Prentice-Hall, 1974, Chapter 23, p.

solveNNLS(Matrix, double[]) - Static method in class woSource.NNLSSolver

solveNNLS(Matrix, Matrix) - Static method in class woSource.NNLSSolver

sort(int[]) - Static method in class woSource.math.ArraysI

quick-sort type.

sort(float[]) - Static method in class woSource.math.ArraysI

sort(Point3D[]) - Static method in class woSource.math.ArraysI

sort(Point4D[]) - Static method in class woSource.math.ArraysI

1/29/11 this sort is not working correctly -- the last 10 items in 150 element list should not be there

sort(NoduleCandidate[]) - Static method in class woSource.math.ArraysI

sort(LIDCnodule[]) - Static method in class woSource.math.ArraysI

WO 2/8/11 sort by patientID.

sortBySliceLoc(ImagePlus) - Static method in class woSource.math.ImgProc

WO 2/2/11 returns the array of orderd indices

sortBySlicePosZ(ImagePlus) - Static method in class woSource.math.ImgProc

sortBySlicePosZ_Time(ImagePlus) - Static method in class woSource.math.ImgProc

WO 2/2/11 returns the array of orderd indices looking at DICOM Image Position Z coord
6/27/2012 added first test to looks for slice labels in Stack's lables array
11/11/2014 secondarily order by image number (for cine image stack).

sortFilesIntoSliceFolders() - Method in class woSource.HeartSegm

sortInsert(int[], int) - Static method in class woSource.math.ArraysI

WO 5/24/2012 will someday want to make this more efficient like the 2D one below

sortInsert(int[][], int[], int, int, int) - Static method in class woSource.math.ArraysI

maxIndex is an index not a count (use A.length-1)
WO 5/23/2012 trying to improve efficiency with center check and split.

sortInsert(float[], float) - Static method in class woSource.math.ArraysI

sortInsert(Point2D[], Point2D) - Static method in class woSource.math.ArraysI

sortInsert(Point3D[], Point3D) - Static method in class woSource.math.ArraysI

sortInsert(Point3Dint[], Point3Dint) - Static method in class woSource.math.ArraysI

sortInsert(Point3D[], Point3D[]) - Static method in class woSource.math.ArraysI

WO 12/23/2010 merge 2 lists, but do not extend beyond the max length

sortInsert(NoduleCandidate[], NoduleCandidate) - Static method in class woSource.math.ArraysI

sortLow2HighInsert(int[][], int[]) - Static method in class woSource.math.ArraysI

Sort low to high.

sortLow2HighInsert(int[][], int[], int) - Static method in class woSource.math.ArraysI

sortLow2HighInsert(int[][], int[], int, int, int) - Static method in class woSource.math.ArraysI

sortMerge(Point3D[], Point3D[]) - Static method in class woSource.math.ArraysI

merge such that result may be longer than either inputs

sortMerge(Point4D[], Point4D[]) - Static method in class woSource.math.ArraysI

merge such that result may be longer than either inputs

sortMerge(NoduleCandidate[], NoduleCandidate[]) - Static method in class woSource.math.ArraysI

spaceWindowsOnScreen() - Method in class woSource.DoseVsIntensity

spaceWindowsOnScreen() - Method in class woSource.HeartSegm

spaceWindowsOnScreen() - Method in class woSource.humanLungSegm

spaceWindowsOnScreen() - Method in class woSource.ImageRegistration

spaceWindowsOnScreen() - Method in class woSource.ImageRegistrationPS

spaceWindowsOnScreen() - Method in class woSource.ImageReviewer

spaceWindowsOnScreen() - Method in class woSource.InteractiveSnake

spaceWindowsOnScreen() - Method in class woSource.MouseMicroCTlungSegm

spaceWindowsOnScreen() - Method in class woSource.noduleDetectionModule

spaceWindowsOnScreen() - Method in class woSource.PulmonaryTrunkSegm

spaceWindowsOnScreen() - Method in class woSource.RatImageAdjuster

spaceWindowsOnScreen() - Method in class woSource.VesselSegm

sph2cart(float, float, float) - Static method in class woSource.math.MathII

return x,y,z in array[3]

sph2cart(double, double, double) - Static method in class woSource.math.MathII

sphericalHarmonicNterms(int[]) - Static method in class woSource.math.MathII

sphericalHarmonicNterms(int, int) - Static method in class woSource.math.MathII

sphericalHarmonicTerm(double, double, double, int, int, int) - Static method in class woSource.math.MathII

WO my spherical harmonics expansions powered by 1/r
1/29/07 problem when r is close to 0 as 1/r blows up.

sphericalHarmonicTerms(double, double, double, int, int) - Static method in class woSource.math.MathII

WO my spherical harmonics expansions powered by 1/r
ref: the Numerical Recipes in C book page 252 the series is: 1 [r,l,m==0], sin(mu)cos(theta) [r=0,l=1,m=-1], cos(mu)[r=0,l=1,m=0], sin(mu)sin(theta)[r=0,l,m=1], ..

sphericalHarmonicTerms(float, float, float, int, int) - Static method in class woSource.math.MathII

sphericalKernel(float) - Static method in class woSource.math.MathII

WO 2/11/11 for radius[mm] spherical kernel.

sphericalKernel(float, float) - Static method in class woSource.math.MathII

sphericalKernel(float, float, float, float, float) - Static method in class woSource.math.MathII

sphericalKernel(float, float, float, float, float, float, float, float) - Static method in class woSource.math.MathII

sphericalKernel(float, float, float, float, float, float, float, float, boolean) - Static method in class woSource.math.MathII

WO 1/30/11 with fractional shifts option & making it a true partial volume calc
rad and padding are in mm
dscale = dimensions of pixel in depth direction [mm]
wscale = dimensions of pixel in width(x) direction [mm]
d,w,h-shifts are in fractions of pixels in d,w,h directions

splitHemiLungs() - Method in class woSource.humanLungSegm

ultimately sets the globally-defined leftLung and rightLung byte[][][] mask arrays \n Works on lungMaskByte and expects on start that lungs are black, outside body and body = white

splitTreeAtConnection(int, int) - Method in class woSource.VesselSegm

11/20/2012 intent is to be given a child branch that is suspected to connect 2 distinct trees
-- where the current tree traversal encountered an instance where the child was larger than its parent and we presume that it jumped from the original tree to branch on the 2nd tree.

sqr(double) - Static method in class woSource.math.MathI

sqr(float) - Static method in class woSource.math.MathI

sqr(int) - Static method in class woSource.math.MathI

sqrt(float[][][]) - Static method in class woSource.math.ArraysI

computes A[i][j]*A[i][j] for each element != matrix multiplication

sqrt() - Method in class woSource.math.Complex

sqrt(Complex) - Static method in class woSource.math.Complex

sqrt(double) - Static method in class woSource.math.MathI

math does not have float version

sqrt(float) - Static method in class woSource.math.MathI

square(Complex) - Static method in class woSource.math.Complex

square() - Method in class woSource.math.Complex

squareAbs(Complex) - Static method in class woSource.math.Complex

squareAbs() - Method in class woSource.math.Complex

ssc - Variable in class woSource.math.ArrayDisplay

Ssnake - Variable in class woSource.InteractiveSnake.Snake

stackprops - Variable in class woSource.math.ArrayDisplay

startDepth - Variable in class woSource.humanLungSegm

startI - Variable in class woSource.lungSnake

startPt - Variable in class woSource.InteractiveSnake.Snake

statsCorrCirc(short[][][], float[][][][]) - Static method in class woSource.math.ImgProc

WO version set corr output size to match input image
also compute NCCC over circular (spherical) region rather than square (cube) because the cube
accentuates far pixels at corners.

statsCorrCirc(short[][][], float[][][][], boolean[][][]) - Static method in class woSource.math.ImgProc

WO version to use mask to speed up computation (which it does)

statsCorrCirc(short[][][], float[][][][], int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

statsCorrCirc(short[][][], float[][][], int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

statsCorrCirc(short[][][], float[][][], boolean[][][], int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

statsCorrCirc(short[][][], float[][][][], boolean[][][], int, int, int, int, int, int) - Static method in class woSource.math.ImgProc

2/16/11 parallel threaded/processor version

statsCorrelation(float[][], float[][]) - Static method in class woSource.math.ImgProc

the statistical correlation coefficient is similar to image correlation, but uses a few more comptuations and is better at finding image features
returns correlation image as 2D array
indices of arrays as [depth][width][height]

statsCorrelation(float[][][], float[][][]) - Static method in class woSource.math.ImgProc

statsCorrelation(int[][], float[][]) - Static method in class woSource.math.ImgProc

statsCorrelation(int[][][], float[][][]) - Static method in class woSource.math.ImgProc

statsCorrelation(float[][][], float[][][][]) - Static method in class woSource.math.ImgProc

PW, 04-01-2002 3D statistical correlation
WO 4/24/02 added ability to do multiple 3D kernels at once
also, knock off the blank edge image elements (slices, columns and rows), thus
resulting corrImage is smaller than original image
This is designed to return the NCCC value computed at each pixel in the original image obtained by moving the kernel over the entire image

statsCorrelation(int[][][], float[][][][]) - Static method in class woSource.math.ImgProc

WO 4/24/02 to do multiple 3D kernels at once, byte version
also, knock off the blank edge image elements (slices, columns and rows)

statsCorrelation(short[][][], float[][][][]) - Static method in class woSource.math.ImgProc

WO 4/24/02 to do multiple 3D kernels at once, short version but return byte in range 0..255

statsCorrelation(int[][], float[][], Point2D[]) - Static method in class woSource.math.ImgProc

WO 5/14/02 version to compute corr only at candidates

statsCorrelation(int[][][], float[][][], Point3D[]) - Static method in class woSource.math.ImgProc

statsCorrelation(int[][][], float[][][][], Point3D[]) - Static method in class woSource.math.ImgProc

statsCorrelation(short[][], float[][], Point2D[]) - Static method in class woSource.math.ImgProc

WO 8/2/02 short version to compute corr only at candidates

statsCorrelation(short[][][], float[][][], Point3D[]) - Static method in class woSource.math.ImgProc

statsCorrelation(short[][][], float[][][], Point3Dint[]) - Static method in class woSource.math.ImgProc

Point3Dint[] version

statsCorrelation(short[][][], float[][][][], Point3D[]) - Static method in class woSource.math.ImgProc

statsCorrelation(short[][][], float[][][][], Point3Dint[]) - Static method in class woSource.math.ImgProc

using Point3Dint[]

stdev(byte[]) - Static method in class woSource.math.ArraysI

stdev(byte[][]) - Static method in class woSource.math.ArraysI

stdev(byte[][][]) - Static method in class woSource.math.ArraysI

stdev(short[]) - Static method in class woSource.math.ArraysI

stdev(short[][]) - Static method in class woSource.math.ArraysI

stdev(short[][][]) - Static method in class woSource.math.ArraysI

stdev(float[]) - Static method in class woSource.math.ArraysI

stdev(float[][]) - Static method in class woSource.math.ArraysI

stdev(float[][][]) - Static method in class woSource.math.ArraysI

StDev_Sep - Variable in class woSource.InteractiveSnake.Snake

stop() - Method in class woSource.MIPSviewer

WO 1/10/2015 I found and fixed a problem that when trying to destroy this MIPsviewer, it calls updater.quit(), which calls updater.inturrupt() and then sets the updater=null and viewAd=null, however the thread could still be inside called the spinning/resetview loop and/or computing the mipsviewbyte such that it will then try to write to the viewAd inside resetview() after the viewAd is killed.

stringGreaterThan(String, String) - Static method in class woSource.math.ArraysI

stringLessThan(String, String) - Static method in class woSource.math.ArraysI

WO my versions of stringarray sorting for comparing filenames whose initial name characters are integers (1.img, 10.img, 2.img, 3,img) the windows sorter messes up these.

subArray(String[], int, int) - Static method in class woSource.math.ArraysI

subArray(Properties[], int, int) - Static method in class woSource.math.ArraysI

subArray(boolean[][], int, int, int, int) - Static method in class woSource.math.ArraysI

subArray(boolean[][], Rectangle) - Static method in class woSource.math.ArraysI

subArray(boolean[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

subArray(boolean[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

subArray(byte[][], int, int, int, int) - Static method in class woSource.math.ArraysI

subArray(byte[][], Rectangle) - Static method in class woSource.math.ArraysI

subArray(byte[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

subArray(byte[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

subArray(int[], int, int) - Static method in class woSource.math.ArraysI

subArray(int[][], int, int, int, int) - Static method in class woSource.math.ArraysI

subArray(int[][], Rectangle) - Static method in class woSource.math.ArraysI

subArray(int[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

subArray(int[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

subArray(short[][], int, int, int, int) - Static method in class woSource.math.ArraysI

subArray(short[][], Rectangle) - Static method in class woSource.math.ArraysI

subArray(short[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

subArray(short[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

subArray(float[], int, int) - Static method in class woSource.math.ArraysI

subArray(float[][], int, int, int, int) - Static method in class woSource.math.ArraysI

subArray(float[][], Rectangle) - Static method in class woSource.math.ArraysI

subArray(float[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

subArray(float[][][], Rectangle3D) - Static method in class woSource.math.ArraysI

subArray(Point3D[], int, int) - Static method in class woSource.math.ArraysI

subArray(Point4D[], int, int) - Static method in class woSource.math.ArraysI

subArray(NoduleCandidate[], int, int) - Static method in class woSource.math.ArraysI

subArray(LIDCnodule[], int, int) - Static method in class woSource.math.ArraysI

subMiddle(short[][], int, int) - Static method in class woSource.math.ArraysI

subMiddle(short[][][], int, int, int) - Static method in class woSource.math.ArraysI

subMiddle(float[], int) - Static method in class woSource.math.ArraysI

subMiddle(float[][], int, int) - Static method in class woSource.math.ArraysI

subMiddle(float[][][], int, int, int) - Static method in class woSource.math.ArraysI

subRect(Rectangle3D) - Method in class woSource.math.Rectangle3D

subsampleDoseField() - Method in class woSource.DoseVsIntensity

WO seems to work properly 2/07
For display -- create a dose array that matches spatially the orig image voxels, for overlay display.

subtractMasks(boolean[][], boolean[][]) - Static method in class woSource.math.ImgProc

if A[i][j] is False, result is False.

subtractMasks(boolean[][][], boolean[][][]) - Static method in class woSource.math.ImgProc

subtractTumorFromLung() - Method in class woSource.DVHCalc

sum(byte[]) - Static method in class woSource.math.ArraysI

WO 1/4/11 return float here since sum can easily be > byte.max

sum(byte[][]) - Static method in class woSource.math.ArraysI

sum(byte[][], int, int, int, int) - Static method in class woSource.math.ArraysI

sum(byte[][][]) - Static method in class woSource.math.ArraysI

sum(byte[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

sum(short[]) - Static method in class woSource.math.ArraysI

sum(short[][]) - Static method in class woSource.math.ArraysI

sum(short[][], int, int, int, int) - Static method in class woSource.math.ArraysI

sum(short[][][]) - Static method in class woSource.math.ArraysI

sum(short[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

sum(int[]) - Static method in class woSource.math.ArraysI

sum(int[][]) - Static method in class woSource.math.ArraysI

sum(int[][], int, int, int, int) - Static method in class woSource.math.ArraysI

sum(int[][][]) - Static method in class woSource.math.ArraysI

sum(int[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

sum(float[]) - Static method in class woSource.math.ArraysI

sum(float[][]) - Static method in class woSource.math.ArraysI

sum(float[][], int, int, int, int) - Static method in class woSource.math.ArraysI

sum(float[][][]) - Static method in class woSource.math.ArraysI

sum(float[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

sumSquares(short[]) - Static method in class woSource.math.ArraysI

sumSquares(short[][]) - Static method in class woSource.math.ArraysI

sumSquares(short[][], int, int, int, int) - Static method in class woSource.math.ArraysI

sumSquares(short[][][]) - Static method in class woSource.math.ArraysI

sumSquares(short[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

sumSquares(float[]) - Static method in class woSource.math.ArraysI

sumSquares(float[][]) - Static method in class woSource.math.ArraysI

sumSquares(float[][], int, int, int, int) - Static method in class woSource.math.ArraysI

sumSquares(float[][][]) - Static method in class woSource.math.ArraysI

sumSquares(float[][][], int, int, int, int, int, int) - Static method in class woSource.math.ArraysI

SurfPts - Variable in class woSource.math.VesselBranch

svdfit(double[][], double[], double[], double[]) - Static method in class woSource.math.OptMath

swap(int[], int[]) - Static method in class woSource.math.ArraysI

swap(float[], float[]) - Static method in class woSource.math.ArraysI

swap(Complex, Complex) - Static method in class woSource.math.Complex

syncCurrentStack() - Method in class woSource.HeartSegm

T

T - Static variable in class woSource.ImageRegistrationPS

t - Variable in class woSource.math.Point4D

t - Variable in class woSource.math.Point4Dint

tagAngle - Variable in class woSource.math.SimTagImageInfo

tagBMfitCoeffs - Variable in class woSource.HeartSegm

tagDefineRect - Variable in class woSource.math.SimTagImageInfo

tagOffset - Variable in class woSource.math.SimTagImageInfo

tagPSfitCoeffs - Variable in class woSource.HeartSegm

tagSearchRect - Variable in class woSource.HeartSegm

tagSpacing - Variable in class woSource.math.SimTagImageInfo

tagWidth - Variable in class woSource.math.SimTagImageInfo

tan() - Method in class woSource.math.Complex

tan(Complex) - Static method in class woSource.math.Complex

tan(double) - Static method in class woSource.math.MathI

tan(float) - Static method in class woSource.math.MathI

tanh() - Method in class woSource.math.Complex

tanh(Complex) - Static method in class woSource.math.Complex

tanh(double) - Static method in class woSource.math.MathI

taper - Variable in class woSource.math.VesselBranch

targetNodsFile - Variable in class woSource.humanLungSegm

templateAd - Variable in class woSource.noduleDetectionModule

terminateOnFuncClose - Variable in class woSource.RatImageAdjuster

terminateOnSegmClose - Variable in class woSource.VesselSegm

terminatingBranch - Variable in class woSource.math.HyperSkelPair

terminatingPt - Variable in class woSource.math.HyperSkelPair

terminatingTree - Variable in class woSource.math.HyperSkelPair

test() - Method in class woSource.math.Polygon2D

thetaOrder - Variable in class woSource.DoseReader

thetaOrder - Variable in class woSource.DoseReader_Oct2012_oldUR

thinnedEdgePts - Variable in class woSource.noduleDetectionModule

this_canvas - Static variable in class woSource.Point3Dviewer

threeDarray(int, int, int) - Static method in class woSource.math.Complex

threeDarray(int, int, int, double, double) - Static method in class woSource.math.Complex

threeDarray(int, int, int, Complex) - Static method in class woSource.math.Complex

threshAd - Variable in class woSource.PulmonaryTrunkSegm

threshAd - Variable in class woSource.VesselSegm

threshold(byte[][], int) - Static method in class woSource.math.ImgProc

threshold(byte[][][], int) - Static method in class woSource.math.ImgProc

threshold(short[][], short) - Static method in class woSource.math.ImgProc

threshold(short[][][], short) - Static method in class woSource.math.ImgProc

threshold(short[][], int) - Static method in class woSource.math.ImgProc

threshold(short[][][], int) - Static method in class woSource.math.ImgProc

threshold(int[][], int) - Static method in class woSource.math.ImgProc

threshold(int[][][], int) - Static method in class woSource.math.ImgProc

threshold(float[][], float) - Static method in class woSource.math.ImgProc

threshold(float[][][], float) - Static method in class woSource.math.ImgProc

timeAt - Variable in class woSource.ImageRegistrationPS

timeFilenames - Variable in class woSource.math.Image3Dinfo

times(Complex, Complex) - Static method in class woSource.math.Complex

times(Complex, double) - Static method in class woSource.math.Complex

times(double, Complex) - Static method in class woSource.math.Complex

times(double, double) - Static method in class woSource.math.Complex

times(Complex) - Method in class woSource.math.Complex

times(double) - Method in class woSource.math.Complex

timesEquals(Complex) - Method in class woSource.math.Complex

timesEquals(double) - Method in class woSource.math.Complex

TLFcoords - Variable in class woSource.math.Image3Dinfo

tmpSurfPts - Variable in class woSource.math.VesselBranch

toBack() - Method in class woSource.math.ArrayDisplay

toBack() - Method in class woSource.MIPSviewer

toBack() - Method in class woSource.MIPSviewerColor

toBoolean(byte[][]) - Static method in class woSource.math.ArraysI

toBoolean(byte[][], int) - Static method in class woSource.math.ArraysI

toBoolean(byte[][][]) - Static method in class woSource.math.ArraysI

toBoolean(byte[][][], int) - Static method in class woSource.math.ArraysI

toBoolean(short[][]) - Static method in class woSource.math.ArraysI

toBoolean(short[][][]) - Static method in class woSource.math.ArraysI

toBoolean(short[][][], int) - Static method in class woSource.math.ArraysI

toByte(boolean[][]) - Static method in class woSource.math.ArraysI

toByte(boolean[][][]) - Static method in class woSource.math.ArraysI

toByte(short[][]) - Static method in class woSource.math.ArraysI

toByte(short[][], int, int) - Static method in class woSource.math.ArraysI

5/19/2012 added this for use with Dicom images where ther Hounsfield unit range should be -1024 to +1024, but can have metal that gives the max value over 3,000, which throws off the scaling.

toByte(int[][]) - Static method in class woSource.math.ArraysI

toByte(short[][][]) - Static method in class woSource.math.ArraysI

toByte(short[][][], int, int) - Static method in class woSource.math.ArraysI

toByte(int[][][]) - Static method in class woSource.math.ArraysI

toByte(float[][]) - Static method in class woSource.math.ArraysI

toByte(float[][][]) - Static method in class woSource.math.ArraysI

toDouble(int[][]) - Static method in class woSource.math.ArraysI

toDouble(int[][][]) - Static method in class woSource.math.ArraysI

toDouble(float[]) - Static method in class woSource.math.ArraysI

toDouble(float[][]) - Static method in class woSource.math.ArraysI

toDouble(float[][][]) - Static method in class woSource.math.ArraysI

toFloat(boolean[][]) - Static method in class woSource.math.ArraysI

toFloat(boolean[][], float) - Static method in class woSource.math.ArraysI

toFloat(boolean[][], float, float) - Static method in class woSource.math.ArraysI

toFloat(boolean[][][]) - Static method in class woSource.math.ArraysI

toFloat(boolean[][][], float) - Static method in class woSource.math.ArraysI

toFloat(boolean[][][], float, float) - Static method in class woSource.math.ArraysI

toFloat(byte[][]) - Static method in class woSource.math.ArraysI

toFloat(byte[][][]) - Static method in class woSource.math.ArraysI

toFloat(short[][]) - Static method in class woSource.math.ArraysI

toFloat(short[][][]) - Static method in class woSource.math.ArraysI

toFloat(int[]) - Static method in class woSource.math.ArraysI

toFloat(int[][]) - Static method in class woSource.math.ArraysI

toFloat(double[]) - Static method in class woSource.math.ArraysI

toFloat(double[][]) - Static method in class woSource.math.ArraysI

toFloat(double[][][]) - Static method in class woSource.math.ArraysI

toFloat(byte) - Static method in class woSource.math.MathI

useful if you don't know what type of number you have

toFloat(short) - Static method in class woSource.math.MathI

toFront() - Method in class woSource.math.ArrayDisplay

toFront() - Method in class woSource.MIPSviewer

toFront() - Method in class woSource.MIPSviewerColor

toFront() - Method in class woSource.Point3Dviewer

toInt(byte[][]) - Static method in class woSource.math.ArraysI

toInt(byte[][][]) - Static method in class woSource.math.ArraysI

toInt(float[]) - Static method in class woSource.math.ArraysI

toInt(float[][]) - Static method in class woSource.math.ArraysI

toInt(float[][][]) - Static method in class woSource.math.ArraysI

toInt(float[][][][]) - Static method in class woSource.math.ArraysI

tortuosity - Variable in class woSource.math.VesselBranch

toShort(Object) - Static method in class woSource.math.ArraysI

toShort(boolean[]) - Static method in class woSource.math.ArraysI

toShort(boolean[], int) - Static method in class woSource.math.ArraysI

toShort(boolean[], int, int) - Static method in class woSource.math.ArraysI

toShort(boolean[][]) - Static method in class woSource.math.ArraysI

toShort(boolean[][], int) - Static method in class woSource.math.ArraysI

toShort(boolean[][], int, int) - Static method in class woSource.math.ArraysI

toShort(boolean[][][]) - Static method in class woSource.math.ArraysI

toShort(boolean[][][], int) - Static method in class woSource.math.ArraysI

toShort(boolean[][][], int, int) - Static method in class woSource.math.ArraysI

toShort(byte[]) - Static method in class woSource.math.ArraysI

toShort(byte[][]) - Static method in class woSource.math.ArraysI

toShort(byte[][][]) - Static method in class woSource.math.ArraysI

toShort(int[]) - Static method in class woSource.math.ArraysI

toShort(int[][]) - Static method in class woSource.math.ArraysI

toShort(int[][][]) - Static method in class woSource.math.ArraysI

toShort(float[][]) - Static method in class woSource.math.ArraysI

toShort(float[][][]) - Static method in class woSource.math.ArraysI

toString() - Method in class woSource.BeadFinder

toString() - Method in class woSource.binClass

toString() - Method in class woSource.create3DTemplate

toString() - Method in class woSource.Deconvolver

toString() - Method in class woSource.DoseReader

toString() - Method in class woSource.DoseReader_Oct2012_oldUR

toString() - Method in class woSource.GradientAnalysis3D

toString() - Method in class woSource.HistoBinAdjuster

toString() - Method in class woSource.HistoMR_registration

toString() - Method in class woSource.ImageRegistration

toString() - Method in class woSource.ImageReviewer

toString() - Method in class woSource.InteractiveSnake.Candidates

toString() - Method in class woSource.InteractiveSnake.Snake

toString() - Method in class woSource.InteractiveSnake.SnakeStack

toString() - Method in class woSource.InteractiveSnake

toString() - Method in class woSource.InteractiveSnake_Hermite

toString() - Method in class woSource.InteractiveSnake_Hermite3D

toString() - Method in class woSource.LesionFinder

toString() - Method in class woSource.LIDCreview

toString() - Method in class woSource.math.ArrayDisplay

toString() - Method in class woSource.math.Complex

toString(Complex) - Static method in class woSource.math.Complex

toString() - Method in class woSource.math.HeartLongAxis

toString() - Method in class woSource.math.HyperSkelPair

toString() - Method in class woSource.math.Image3Dinfo

toString() - Method in class woSource.math.LIDCnodule

toString(int, int) - Static method in class woSource.math.MathI

goal to add right number of leading zeros

toString() - Method in class woSource.math.NoduleCandidate

toString() - Method in class woSource.math.Point2D

toString() - Method in class woSource.math.Point3D

toString() - Method in class woSource.math.Point3Dint

toString() - Method in class woSource.math.Point4D

toString() - Method in class woSource.math.Point4Dint

toString() - Method in class woSource.math.Polygon2D

toString() - Method in class woSource.math.Polygon3D

toString() - Method in class woSource.math.Polygon3Dint

toString() - Method in class woSource.math.Rectangle3D

toString() - Method in class woSource.math.SimTagImageInfo

toString() - Method in class woSource.math.VesselBranch

toString() - Method in class woSource.math.VesselTree

toString(boolean) - Method in class woSource.math.VesselTree

toString() - Method in class woSource.MotionBlur

toString() - Method in class woSource.MouseLungSegmentor

toString() - Method in class woSource.VolOverlap

toString() - Method in class woSource.WindowLevelAdjuster

total_energy(Point2D[]) - Method in class woSource.InteractiveSnake.Snake

traceCenterline(Point3Dint) - Method in class woSource.VesselSegm

traceCenterlines(Point3Dint[], int) - Method in class woSource.VesselSegm

transform(short[][][], float, float, float, float, float, float, Rectangle3D) - Static method in class woSource.math.ImgProc

this is used by ArrayDisplay.overlapImage()

transform(short[][], float, float, float) - Static method in class woSource.math.ImgProc

WO 12/17/09 2D version, but without ROI usage

transformConPoints(float[][], float, float, float) - Method in class woSource.Point3Dviewer

transformedAD - Variable in class woSource.ImageRegistration

transformFromHeartCoords(float[][][][], boolean[][][]) - Method in class woSource.math.HeartLongAxis

transformImage_mm(short[][], Properties, float, float, float) - Static method in class woSource.math.ImgProc

WO 3/10/09 These funcs transform the image w/r/2 its own 3D coord system and outputs it into the pixel system of the target image.

transformImage_mm(short[][][], Properties[], Rectangle3D, ImageRegistration, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

version that creates and returns the transformed Image.
WO 4/25/20913 This seems to be working correctly.

transformImage_mm(short[][][], Properties[], Rectangle3D, ImageRegistration, Properties[], Rectangle3D, short[][][]) - Static method in class woSource.math.ImgProc

transformImage_mm(short[][][], Properties[], Rectangle3D, ImageRegistration, Properties[], Rectangle3D, short[][][], boolean) - Static method in class woSource.math.ImgProc

transformImage_mm(short[][][], Properties[], Rectangle3D, float, float, float, float, float, float, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

transformImage_mm(short[][][], Properties[], Rectangle3D, float, float, float, float, float, float, float, float, float, Properties[], Rectangle3D) - Static method in class woSource.math.ImgProc

version that creates and returns the transformed Image.
WO 4/25/20913 This seems to be working correctly.

transformImage_mm(short[][][], Properties[], Rectangle3D, float, float, float, float, float, float, Properties[], Rectangle3D, short[][][]) - Static method in class woSource.math.ImgProc

transformImage_mm(short[][][], Properties[], Rectangle3D, float, float, float, float, float, float, float, float, float, Properties[], Rectangle3D, short[][][], boolean) - Static method in class woSource.math.ImgProc

version with resulting transformed Image as parameter for case when need to save memory upon multiple calls.
WO 4/25/20913 This seems to be working correctly.

transformPixelToScannerCoords(int[], int) - Method in class woSource.math.Image3Dinfo

transformPixelToScannerCoords(float[], int) - Method in class woSource.math.Image3Dinfo

transformPixelToScannerCoords(float, float, int) - Method in class woSource.math.Image3Dinfo

transformPixelToScannerCoords(Point3D) - Method in class woSource.math.Image3Dinfo

transformPixelToScannerCoords(float[][][], int, boolean[][][]) - Method in class woSource.math.Image3Dinfo

transformPixelToScannerCoords(float[][][][], boolean[][][]) - Method in class woSource.math.Image3Dinfo

transformScannerToNearestPixelCoords(float[][][][], boolean[][][]) - Method in class woSource.math.Image3Dinfo

transformScannerToPixelCoords(float[][][]) - Method in class woSource.math.Image3Dinfo

transformScannerToPixelCoords(float[][][][], boolean[][][]) - Method in class woSource.math.Image3Dinfo

transformToHeartCoords(float[][][][], boolean[][][]) - Method in class woSource.math.HeartLongAxis

transformToHeartCoords(float[]) - Method in class woSource.math.HeartLongAxis

transformToHeartCoords(Point3D) - Method in class woSource.math.HeartLongAxis

transformToHeartCoords(float[][]) - Method in class woSource.math.HeartLongAxis

transformToHeartCoords(float[][], int) - Method in class woSource.math.HeartLongAxis

transformToImageSpace(Properties[], float, Roi) - Method in class woSource.DoseReader_Oct2012_oldUR

transpose(byte[][]) - Static method in class woSource.math.ArraysI

transpose(short[][]) - Static method in class woSource.math.ArraysI

transpose(float[][]) - Static method in class woSource.math.ArraysI

transpose(double[][]) - Static method in class woSource.math.ArraysI

transposedMinus(double) - Method in class woSource.math.Complex

transposedOver(double) - Method in class woSource.math.Complex

traverseToFindTreeTop(int) - Method in class woSource.VesselSegm

treeFrom - Variable in class woSource.math.HyperSkelPair

TreeMask - Variable in class woSource.math.VesselTree

TreeTop - Variable in class woSource.math.VesselTree

treeTops - Variable in class woSource.PulmonaryTrunkSegm

triangleArea(float, float, float, float, float, float) - Static method in class woSource.math.MathII

uses Heron's formula

triangleNormal(float[], float[], float[]) - Static method in class woSource.math.MathII

want 3D outward normal to 3D triangle defined by 3 points, with the outwardness set by point order and RHR

trimBranchEndPts(int, int, boolean, float) - Method in class woSource.VesselSegm

trimSmoothEndPts(int, int, boolean, float) - Method in class woSource.VesselSegm

trimStubs() - Method in class woSource.math.VesselTree

trimTreeStubs() - Method in class woSource.VesselSegm

intent is to go through all the tree branches and remove any branches with only 1 point that are not a looped-to location.

trunkMaxThresh - Variable in class woSource.VesselSegm

trunkMinThresh - Variable in class woSource.VesselSegm

trunkSeedx - Variable in class woSource.VesselSegm

trunkSeedy - Variable in class woSource.VesselSegm

trunkSeedz - Variable in class woSource.VesselSegm

trunkSkelStartPt - Variable in class woSource.VesselSegm

turnOffListeners() - Method in class woSource.math.ArrayDisplay

this was an attempt to avoid invoking a GUI function repeatedly before the previous function call had time to complete, hoping that this would absolve a hanging bug with snakes.

turnOffPtLabels() - Method in class woSource.MIPSviewerColor

turnOffSliceScrollWithWheel - Variable in class woSource.ScreenSelectorCanvas

turnOnListeners() - Method in class woSource.math.ArrayDisplay

turnONPtLabels() - Method in class woSource.MIPSviewerColor

twoDarray(int, int) - Static method in class woSource.math.Complex

twoDarray(int, int, double, double) - Static method in class woSource.math.Complex

twoDarray(int, int, Complex) - Static method in class woSource.math.Complex

twoPiJay() - Static method in class woSource.math.Complex

U

unhide() - Method in class woSource.math.ArrayDisplay

unhideDialog() - Method in class woSource.GenericRecallableDialog

unhighlightButton(int) - Method in class woSource.GenericRecallableDialog

unwrapImg(short[][][], int, int, int) - Method in class woSource.unwrapMR_stack

unwrapMR_stack - Class in woSource

unwrapMR_stack() - Constructor for class woSource.unwrapMR_stack

update(int, InteractiveSnake.Snake) - Method in class woSource.InteractiveSnake.SmoothSnake

update(int, int, float, float, float, float) - Method in class woSource.math.SimTagImageInfo

update(float, float, float, float, Rectangle) - Method in class woSource.math.SimTagImageInfo

update(int, int, float, float, float, float, Rectangle) - Method in class woSource.math.SimTagImageInfo

update(Graphics) - Method in class woSource.ScreenSelectorCanvas

UpdateAttributes(float, float, float, float, int, boolean) - Method in class woSource.InteractiveSnake.Snake

UpdateAttributes(float, float, float, float, int, boolean) - Method in class woSource.InteractiveSnake.SnakeStack

public void Draw(Graphics gr, ImageCanvas canvas) { snakes[cur_snake].Draw(gr, canvas); /* need 3d display GUI * } public void Draw(Graphics gr, ScreenSelectorCanvas canvas) { snakes[cur_snake].Draw(gr, canvas); }

UpdateAttributes(float, float, float, float, int, boolean) - Method in class woSource.InteractiveSnake

UpdateAttributes() - Method in class woSource.InteractiveSnake_Hermite

UpdateAttributes() - Method in class woSource.InteractiveSnake_Hermite3D

updateConCoords(int, int, int, int, int, float[][]) - Method in class woSource.Point3Dviewer

updateCumRot(float, float) - Method in class woSource.Point3Dviewer

updateCumRot(float, float, float) - Method in class woSource.Point3Dviewer

updateFullWindow - Variable in class woSource.ScreenSelectorCanvas

updateMarkingPanel() - Method in class woSource.ImageReviewer

updateMIPs(boolean[][][]) - Method in class woSource.PulmonaryTrunkSegm

updateMIPs(byte[][][]) - Method in class woSource.PulmonaryTrunkSegm

updateMIPs(byte[][][], byte[][][]) - Method in class woSource.PulmonaryTrunkSegm

updateMIPs() - Method in class woSource.RatImageAdjuster

updateMIPs(boolean[][][]) - Method in class woSource.VesselSegm

updateMIPs(byte[][][]) - Method in class woSource.VesselSegm

updateMIPs(byte[][][], byte[][][]) - Method in class woSource.VesselSegm

updatePScoeffsArray(int, int, int, int) - Method in class woSource.ImageRegistrationPS

updatePt3Dview() - Method in class woSource.Point3Dviewer

updatePtCoords(float[][]) - Method in class woSource.Point3Dviewer

updatePtCoords(float[][][]) - Method in class woSource.Point3Dviewer

updater - Variable in class woSource.MIPSviewer

updater - Variable in class woSource.Point3Dviewer

updateRegDisplay(String) - Method in class woSource.HistoMR_registration

updateRegDisplay(String) - Method in class woSource.ImageRegistration

updateRegDisplay() - Method in class woSource.ImageRegistrationPS

UpdateScreen() - Method in class woSource.BeadFinder

UpdateScreen() - Method in class woSource.ImageReviewer

UpdateScreen() - Method in class woSource.InteractiveSnake

invoked most commonly within here, but also by ScreenSelectorCanvas.updateScreen()

UpdateScreen() - Method in class woSource.InteractiveSnake_Hermite

UpdateScreen() - Method in class woSource.InteractiveSnake_Hermite3D

UpdateScreen() - Method in class woSource.LIDCreview

UpdateScreen() - Method in class woSource.Point3Dviewer

UpdateScreen() - Method in class woSource.ScreenSelectorClass

updateScrollBars(int[], GenericRecallableDialog) - Method in class woSource.HistoBinAdjuster

UpdateSelection(int, int, String) - Method in class woSource.ImageReviewer

UpdateSelection(int, int, String) - Method in class woSource.InteractiveSnake

UpdateSelection(int, int, String) - Method in class woSource.InteractiveSnake_Hermite

UpdateSelection(int, int, String) - Method in class woSource.InteractiveSnake_Hermite3D

UpdateSelection(int, int, String) - Method in class woSource.MIPSviewer

UpdateSelection(int, int, String) - Method in class woSource.MouseLungSegmentor

UpdateSelection(int, int, String) - Method in class woSource.MouseMicroCTlungSegm

UpdateSelection(int, int, String) - Method in class woSource.Point3Dviewer

UpdateSelection(int, int, String) - Method in class woSource.ScreenSelectorClass

UpdateSelectionImageReviewer(int, int, String) - Method in class woSource.ImageReviewer

updateSnakeStacksForNewSlice(int, int, ArrayDisplay) - Method in class woSource.HeartSegm

updateSphericalHarmonicCoeffsArray(float[], int, int, int, int) - Static method in class woSource.math.MathII

updateThreshold() - Method in class woSource.AirwaySegm

updateThreshold() - Method in class woSource.PulmonaryTrunkSegm

updateThreshold() - Method in class woSource.VesselSegm

updateThresholds() - Method in class woSource.ColonSegm

UpdateToAd(ArrayDisplay) - Method in class woSource.InteractiveSnake.SnakeStack

upperConnThresh - Variable in class woSource.PulmonaryTrunkSegm

useAdditionalDrawingAD - Variable in class woSource.InteractiveSnake

UseDisconnectedEnds - Variable in class woSource.InteractiveSnake.Snake

useDistanceTransform - Variable in class woSource.VesselSegm

UseFixedEnds - Variable in class woSource.InteractiveSnake.Snake

useTaper - Variable in class woSource.math.VesselTree

V

validate() - Method in class woSource.math.ArrayDisplay

value - Variable in class woSource.math.Point2D

value - Variable in class woSource.math.Point3D

value - Variable in class woSource.math.Point3Dint

value - Variable in class woSource.math.Point4D

value - Variable in class woSource.math.Point4Dint

valueOf(String) - Static method in class woSource.math.Complex

varname - Variable in class woSource.math.Point4D

varname - Variable in class woSource.math.Point4Dint

Vcross(Point2D, Point2D) - Static method in class woSource.math.MathII

Vcross(float[], float[]) - Static method in class woSource.math.MathII

Vcross(double[], double[]) - Static method in class woSource.math.MathII

Vcross(Point3D, Point3D) - Method in class woSource.math.Point3D

Vcross(Point4D, Point4D) - Method in class woSource.math.Point4D

Vcross(Point4Dint, Point4Dint) - Method in class woSource.math.Point4Dint

VcrossMag(Point2D, Point2D) - Static method in class woSource.math.MathII

vers() - Method in class woSource.math.Complex

vers(Complex) - Static method in class woSource.math.Complex

VertexPts - Variable in class woSource.FEelemClass

veryFirstReadInAllImages() - Method in class woSource.HeartSegm

VesselBranch - Class in woSource.math

VesselBranch() - Constructor for class woSource.math.VesselBranch

VesselBranch(int, int, int, float, float) - Constructor for class woSource.math.VesselBranch

VesselBranch(int, VesselBranch) - Constructor for class woSource.math.VesselBranch

vesselRect - Variable in class woSource.VesselSegm

vesselsegm - Variable in class woSource.PulmonaryTrunkSegm

VesselSegm - Class in woSource

bug: when do airway segm and then return, seed selection for vessels is limited to the original window size.

VesselSegm() - Constructor for class woSource.VesselSegm

VesselTree - Class in woSource.math

WO VesselTree is a class/data structure to describe a tree structure containing many branches.

VesselTree(float, float) - Constructor for class woSource.math.VesselTree

VesselTree(int, float, float) - Constructor for class woSource.math.VesselTree

VesselTree(int, VesselTree) - Constructor for class woSource.math.VesselTree

VesselTree.OptBrNodThread - Class in woSource.math

This class is defined to run function OptBrNodes in //
WO 4/11/2012 All threads work with the same global origImg, but they only access this image and do not change it.

VesselTree.OptBrRadThread - Class in woSource.math

This class is defined to run function OptBrRadius in //
WO 4/11/2012 This works by defining a unique Roi for each thread to work on.

view3DAd - Variable in class woSource.Point3Dviewer

viewTransformedImage - Variable in class woSource.ImageRegistration

VisualHumanConvert2Dicom - Class in woSource

VisualHumanConvert2Dicom() - Constructor for class woSource.VisualHumanConvert2Dicom

vlen(float[]) - Static method in class woSource.math.MathII

vlen(double[]) - Static method in class woSource.math.MathII

vlength(float[]) - Static method in class woSource.math.MathII

vlength(double[]) - Static method in class woSource.math.MathII

Vminus(float[], float[]) - Static method in class woSource.math.MathII

Vmult(float, float[]) - Static method in class woSource.math.MathII

vnorm(float[]) - Static method in class woSource.math.MathII

vnorm(Point3D) - Static method in class woSource.math.MathII

VolOverlap - Class in woSource

VolOverlap() - Constructor for class woSource.VolOverlap

volume() - Method in class woSource.math.Rectangle3D

voxelEndoLambdas - Variable in class woSource.math.SeriesImagesClass

Vplus(float[], float[]) - Static method in class woSource.math.MathII

element-wise addition.

W

W - Static variable in class woSource.ImageRegistration

wantQuit - Variable in class woSource.MIPSviewer.Updater

wantQuit - Variable in class woSource.Point3Dviewer.Updater

wasContoured - Variable in class woSource.InteractiveSnake.Snake

wasDicom - Variable in class woSource.DoseReader

wasDicom - Variable in class woSource.DoseReader_Oct2012_oldUR

wasReadIn - Variable in class woSource.ImageRegistration

wasReadIn - Variable in class woSource.math.HeartLongAxis

wasTraversed - Variable in class woSource.math.VesselBranch

WelchWindow(int, int, float) - Static method in class woSource.math.MathII

Welch window: I changed it some, replacing 'b' with 'cutoff',
and 'a' with 'N' ('a' was usually set to N/2)

WelchWindow(int, float, float) - Static method in class woSource.math.MathII

WelchWindow(float, float, float) - Static method in class woSource.math.MathII

WEST - Variable in class woSource.GenericRecallableDialog

Width - Variable in class woSource.DoseReader

Width - Variable in class woSource.DoseReader_Oct2012_oldUR

WIDTH - Static variable in class woSource.math.ArrayDisplay

Width - Variable in class woSource.math.ArrayDisplay

width - Variable in class woSource.math.Rectangle3D

width - Variable in class woSource.math.SeriesImagesClass

Wiener1D(float[]) - Method in class woSource.Deconvolver

Wiener3D(float[][][]) - Method in class woSource.Deconvolver

windowHasFocus - Variable in class woSource.ScreenSelectorCanvas

WindowLevelAdjuster - Class in woSource

WindowLevelAdjuster() - Constructor for class woSource.WindowLevelAdjuster

winLevel() - Method in class woSource.MIPSviewer

winLevel() - Method in class woSource.MIPSviewerColor

winLevel() - Method in class woSource.Point3Dviewer

withContrast - Variable in class woSource.math.VesselTree

woEndsWithFilter - Class in woSource.math

woEndsWithFilter(String) - Constructor for class woSource.math.woEndsWithFilter

working_canvas - Static variable in class woSource.ImageReviewer

working_canvas - Variable in class woSource.math.ArrayDisplay

working_canvas - Static variable in class woSource.MouseLungSegmentor

working_canvas - Static variable in class woSource.MouseMicroCTlungSegm

working_display - Variable in class woSource.math.ArrayDisplay

working_frame - Variable in class woSource.math.ArrayDisplay

working_graphics - Variable in class woSource.math.ArrayDisplay

working_ip - Variable in class woSource.math.ArrayDisplay

working_ip_stack - Variable in class woSource.math.ArrayDisplay

working_stack - Variable in class woSource.math.ArrayDisplay

working_window - Variable in class woSource.math.ArrayDisplay

woSource - package woSource

woSource.math - package woSource.math

Write() - Method in class woSource.DoseReader

Write() - Method in class woSource.DoseReader_Oct2012_oldUR

write() - Method in class woSource.ImageRegistration

write(String, int) - Method in class woSource.ImageRegistrationPS

Write() - Method in class woSource.InteractiveSnake.Snake

Write(String) - Method in class woSource.InteractiveSnake.SnakeStack

write(byte[][][], String) - Static method in class woSource.math.ArraysI

write(byte[][][], String, boolean) - Static method in class woSource.math.ArraysI

write(byte[][][], int, int, int, String, boolean) - Static method in class woSource.math.ArraysI

write(short[][][], String) - Static method in class woSource.math.ArraysI

write(short[][][], String, boolean) - Static method in class woSource.math.ArraysI

write(short[][][], int, int, int, String, boolean) - Static method in class woSource.math.ArraysI

write(int[], String) - Static method in class woSource.math.ArraysI

write(int[], String, boolean) - Static method in class woSource.math.ArraysI

write(int[], int, String) - Static method in class woSource.math.ArraysI

write(int[], int, String, boolean) - Static method in class woSource.math.ArraysI

write(int[][], String) - Static method in class woSource.math.ArraysI

write(int[][], String, boolean) - Static method in class woSource.math.ArraysI

write(int[][], int, int, String, boolean) - Static method in class woSource.math.ArraysI

write(int[][][], String) - Static method in class woSource.math.ArraysI

write(int[][][], String, boolean) - Static method in class woSource.math.ArraysI

write(int[][][], int, int, int, String, boolean) - Static method in class woSource.math.ArraysI

write(float[], String) - Static method in class woSource.math.ArraysI

write(float[], int, String) - Static method in class woSource.math.ArraysI

write(float[], float[], String) - Static method in class woSource.math.ArraysI

WO 10/2/07 great, we can write out 2 arrays but cannot read in and save 2 arrays

write(float[], float[], int, String) - Static method in class woSource.math.ArraysI

write(float[], float[], float[], String) - Static method in class woSource.math.ArraysI

write(float[], float[], float[], int, String) - Static method in class woSource.math.ArraysI

write(float[][][], String) - Static method in class woSource.math.ArraysI

write(float[][][], String, boolean) - Static method in class woSource.math.ArraysI

write(float[][][], int, int, int, String, boolean) - Static method in class woSource.math.ArraysI

write(float[][][][], String) - Static method in class woSource.math.ArraysI

write(float[][][][], String, boolean) - Static method in class woSource.math.ArraysI

write(float[][][][], int, int, int, int, String, boolean) - Static method in class woSource.math.ArraysI

write(float[][][][][], String) - Static method in class woSource.math.ArraysI

write(float[][][][][], String, boolean) - Static method in class woSource.math.ArraysI

write(float[][][][][], int, int, int, int, int, String, boolean) - Static method in class woSource.math.ArraysI

works but output files can be very large (~60M for eigenvectors of DTI).

write(double[], String) - Static method in class woSource.math.ArraysI

write(double[], int, String) - Static method in class woSource.math.ArraysI

write(Point2D[], String) - Static method in class woSource.math.ArraysI

write(Point2D[], int, String) - Static method in class woSource.math.ArraysI

write(Point2D[][], String) - Static method in class woSource.math.ArraysI

write(Point3D[], String) - Static method in class woSource.math.ArraysI

write(Point3D[], int, String) - Static method in class woSource.math.ArraysI

write(Point3D[], int, String, boolean) - Static method in class woSource.math.ArraysI

write(Point3D[][], String) - Static method in class woSource.math.ArraysI

write(Point3D[][][], String) - Static method in class woSource.math.ArraysI

write(Point4D[], String) - Static method in class woSource.math.ArraysI

write(Point4D[], int, String) - Static method in class woSource.math.ArraysI

write(Point4D[], String, boolean) - Static method in class woSource.math.ArraysI

write(Point4D[], int, String, boolean) - Static method in class woSource.math.ArraysI

write(Point4D[][][], String) - Static method in class woSource.math.ArraysI

write(Polygon2D, String) - Static method in class woSource.math.ArraysI

write(Polygon2D[], String) - Static method in class woSource.math.ArraysI

write(Polygon3D[], String) - Static method in class woSource.math.ArraysI

write(Polygon3Dint[], String) - Static method in class woSource.math.ArraysI

write(LIDCnodule[], String) - Static method in class woSource.math.ArraysI

write(LIDCnodule[], int, String) - Static method in class woSource.math.ArraysI

write(LIDCnodule[][], String) - Static method in class woSource.math.ArraysI

write(NoduleCandidate[], String) - Static method in class woSource.math.ArraysI

write(NoduleCandidate[], String, boolean) - Static method in class woSource.math.ArraysI

write(NoduleCandidate[], int, String) - Static method in class woSource.math.ArraysI

write(NoduleCandidate[], int, String, boolean) - Static method in class woSource.math.ArraysI

write(NoduleCandidate[][], String) - Static method in class woSource.math.ArraysI

write(NoduleCandidate[][], String, boolean) - Static method in class woSource.math.ArraysI

write(String, String) - Method in class woSource.math.Rectangle3D

write_sparse(float[][][][], String) - Static method in class woSource.math.ArraysI

write_sparse(float[][][][], String, boolean) - Static method in class woSource.math.ArraysI

write_sparse(float[][][][], int, int, int, int, String, boolean) - Static method in class woSource.math.ArraysI

write_sparse(float[][][][][], String) - Static method in class woSource.math.ArraysI

write_sparse(float[][][][][], String, boolean) - Static method in class woSource.math.ArraysI

write_sparse(float[][][][][], int, int, int, int, int, String, boolean) - Static method in class woSource.math.ArraysI

writeAllHeartLAinfo() - Method in class woSource.HeartSegm

writeAllTreesSTL() - Method in class woSource.VesselSegm

writeBiggestTreeParams() - Method in class woSource.VesselSegm

writeBiggestTreeParams(String) - Method in class woSource.VesselSegm

writeDefImgTrans() - Method in class woSource.ImageRegistration

WO 5/13/09 want to stick the dicom headers from the refImages onto the defImgTrans data this is working for MRI T1 data at least.

writeDicom() - Method in class woSource.ConvertToDicom

writeDicomInfo(String, String, String[][]) - Method in class woSource.DicomAnon

writeImageFile(byte[][], String) - Static method in class woSource.math.ImgProc

writeImageFile(short[][], String) - Static method in class woSource.math.ImgProc

writeImageFiles(boolean[][][], String, String[], String) - Static method in class woSource.math.ImgProc

writeImageFiles(byte[][][], String, String[], String) - Static method in class woSource.math.ImgProc

writeImageFiles(short[][][], String, String[], String) - Static method in class woSource.math.ImgProc

writeInfo(String) - Method in class woSource.math.HeartLongAxis

writeInfo(String) - Method in class woSource.math.SimTagImageInfo

writeMaskImgs() - Method in class woSource.MouseLungSegmentor

writeParams() - Method in class woSource.HistoHisto_reg

writeStudyInfo() - Method in class woSource.HeartSegm

X

X - Static variable in class woSource.ImageRegistrationPS

X - Static variable in class woSource.math.ArrayDisplay

X - Static variable in class woSource.math.ArraysI

X - Static variable in class woSource.math.HeartLongAxis

X - Static variable in class woSource.math.Image3Dinfo

x - Variable in class woSource.math.LIDCnodule

X - Static variable in class woSource.math.MathI

X - Static variable in class woSource.math.MathII

x - Variable in class woSource.math.NoduleCandidate

X - Variable in class woSource.math.OptMath

x - Variable in class woSource.math.Point2D

x - Variable in class woSource.math.Point3D

x - Variable in class woSource.math.Point3Dint

x - Variable in class woSource.math.Point4D

x - Variable in class woSource.math.Point4Dint

x - Variable in class woSource.math.Rectangle3D

xpoints - Variable in class woSource.math.Polygon2D

xpoints - Variable in class woSource.math.Polygon3D

xpoints - Variable in class woSource.math.Polygon3Dint

Y

Y - Static variable in class woSource.ImageRegistrationPS

Y - Static variable in class woSource.math.ArrayDisplay

Y - Static variable in class woSource.math.ArraysI

Y - Static variable in class woSource.math.HeartLongAxis

Y - Static variable in class woSource.math.Image3Dinfo

y - Variable in class woSource.math.LIDCnodule

Y - Static variable in class woSource.math.MathI

Y - Static variable in class woSource.math.MathII

y - Variable in class woSource.math.NoduleCandidate

Y - Variable in class woSource.math.OptMath

y - Variable in class woSource.math.Point2D

y - Variable in class woSource.math.Point3D

y - Variable in class woSource.math.Point3Dint

y - Variable in class woSource.math.Point4D

y - Variable in class woSource.math.Point4Dint

y - Variable in class woSource.math.Rectangle3D

ypoints - Variable in class woSource.math.Polygon2D

ypoints - Variable in class woSource.math.Polygon3D

ypoints - Variable in class woSource.math.Polygon3Dint

Z

Z - Static variable in class woSource.ImageRegistrationPS

Z - Static variable in class woSource.math.ArrayDisplay

Z - Static variable in class woSource.math.ArraysI

Z - Static variable in class woSource.math.HeartLongAxis

Z - Static variable in class woSource.math.Image3Dinfo

Z - Static variable in class woSource.math.MathI

Z - Static variable in class woSource.math.MathII

Z - Variable in class woSource.math.OptMath

z - Variable in class woSource.math.Point3D

z - Variable in class woSource.math.Point3Dint

z - Variable in class woSource.math.Point4D

z - Variable in class woSource.math.Point4Dint

z - Variable in class woSource.math.Rectangle3D

zero() - Static method in class woSource.math.Complex

zeros(int[]) - Static method in class woSource.math.ArraysI

returns array of zeros of same dims as A

zeros(int[][]) - Static method in class woSource.math.ArraysI

zeros(int[][][]) - Static method in class woSource.math.ArraysI

zeros(int[][][][]) - Static method in class woSource.math.ArraysI

zeros(boolean[]) - Static method in class woSource.math.ArraysI

zeros(boolean[][]) - Static method in class woSource.math.ArraysI

zeros(boolean[][][]) - Static method in class woSource.math.ArraysI

zeros(float[]) - Static method in class woSource.math.ArraysI

zeros(float[][]) - Static method in class woSource.math.ArraysI

zeros(float[][][]) - Static method in class woSource.math.ArraysI

zeros(float[][][][]) - Static method in class woSource.math.ArraysI

zeros(float[][][][][][]) - Static method in class woSource.math.ArraysI

zeros(byte[]) - Static method in class woSource.math.ArraysI

zeros(byte[][]) - Static method in class woSource.math.ArraysI

zeros(byte[][][]) - Static method in class woSource.math.ArraysI

zeros(short[]) - Static method in class woSource.math.ArraysI

zeros(short[][]) - Static method in class woSource.math.ArraysI

zeros(short[][][]) - Static method in class woSource.math.ArraysI

zeros(short[][][][]) - Static method in class woSource.math.ArraysI

zeros(double[]) - Static method in class woSource.math.ArraysI

zeros(double[][]) - Static method in class woSource.math.ArraysI

zeros(double[][][]) - Static method in class woSource.math.ArraysI

zoomIn() - Method in class woSource.math.ArrayDisplay

zooms in to next zoom level and makes the window bigger (checks if getting too big) x,y, are pixel coords of center of where image is to be

zoomIn() - Method in class woSource.MIPSviewer

zoomIn() - Method in class woSource.MIPSviewerColor

zoomIn() - Method in class woSource.Point3Dviewer

zoomOut() - Method in class woSource.math.ArrayDisplay

zooms out to next zoom level and makes the window smaller (checks if getting too small) x,y, are pixel coords of center of where image is to be.

zoomOut() - Method in class woSource.MIPSviewer

zoomOut() - Method in class woSource.MIPSviewerColor

zoomToRoi() - Method in class woSource.math.ArrayDisplay

2/28/2013 zooms in to match the size of the Roi, without changing the window size

zoomToRoi(Roi) - Method in class woSource.math.ArrayDisplay

zoomToRoi(Rectangle) - Method in class woSource.math.ArrayDisplay

zpoints - Variable in class woSource.math.Polygon3D

zpoints - Variable in class woSource.math.Polygon3Dint

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