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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