woSource

Class LIDCreview

java.lang.Object

woSource.ScreenSelectorClass

woSource.ImageReviewer

woSource.LIDCreview

All Implemented Interfaces:

ij.plugin.PlugIn

public class LIDCreview
extends ImageReviewer
implements ij.plugin.PlugIn

Field Summary

Fields inherited from class woSource.ImageReviewer

working_canvas

Constructor Summary

Constructors

Constructor and Description
LIDCreview()

Method Summary

Modifier and Type	Method and Description
float[][][][]	addWall2Template(float[][][][] A, float k, float i, float j, float dilateSize)
float[][][][]	addWall2Template(float[][][][] A, NoduleCandidate cand, float dilateSize)
float[][][]	addWall2Template(float[][][] A, float k, float i, float j, float dilateSize)
float[][][]	addWall2Template(float[][][] A, NoduleCandidate cand, float dilateSize)
void	applyTemplates()
float[][][][]	calcKall(float radius, float wpadding, float dscale, float wscale, float hscale) 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.
float[][][][]	calcKall(float radius, float wpadding, float dscale, float wscale, float hscale, float shiftd, float shiftw, float shifth)
float	candidateSep(NoduleCandidate A, NoduleCandidate B) 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.
float	candidateSep(Point3D A, NoduleCandidate B)
void	customButFunc()
void	customChoiceFunc()
void	get3DviewOfNodule()
void	getLungMask()
void	getObjectMask()
void	initPtNodules()
boolean	kernelHitsChestWall(NoduleCandidate c, float[][][] A)
void	NCCCoptLoc(int candStart, int candEnd)
void	NCCCoptRadii(int candStart, int candEnd, int iter) 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
void	optParams()
protected void	redisplay()
void	run(java.lang.String arg) This method is called when the plugin is loaded.
void	setNewSlice()
void	setNewStudy()
void	setupImg()
java.lang.String	toString()
void	UpdateScreen()

Methods inherited from class woSource.ImageReviewer

adjustCurSlice, cropToObjectROI, findClosestMark, get3Dview, get3DviewOfmark, getObjectMaskFromFiles, getObjectMaskFromFiles, getPtInputDirInfo, resetwidgets, run, runGUI, setGUIWinLevelWidgets, setupImg, setupImg, setupImg, spaceWindowsOnScreen, updateMarkingPanel, UpdateSelection, UpdateSelectionImageReviewer

Methods inherited from class woSource.ScreenSelectorClass

keyPressed, mouseDragged, mouseMoved, mousePressed, mouseReleased

Methods inherited from class java.lang.Object

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

Constructor Detail

LIDCreview

public LIDCreview()

Method Detail

run

public void run(java.lang.String arg)

Description copied from interface: ij.plugin.PlugIn

This method is called when the plugin is loaded. 'arg', which may be blank, is the argument specified for this plugin in IJ_Props.txt.

Specified by:

run in interface ij.plugin.PlugIn

Overrides:

run in class ImageReviewer

customButFunc

public void customButFunc()

Overrides:

customButFunc in class ImageReviewer

customChoiceFunc

public void customChoiceFunc()

Overrides:

customChoiceFunc in class ImageReviewer

setNewSlice

public void setNewSlice()

Overrides:

setNewSlice in class ImageReviewer

setNewStudy

public void setNewStudy()

Overrides:

setNewStudy in class ImageReviewer

get3DviewOfNodule

public void get3DviewOfNodule()

UpdateScreen

public void UpdateScreen()

Overrides:

UpdateScreen in class ImageReviewer

optParams

public void optParams()

applyTemplates

public void applyTemplates()

candidateSep

public float candidateSep(NoduleCandidate A,
                          NoduleCandidate B)

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. OpenDialog.setDefaultDirectory(LIDCstudyInputDir); new FolderOpener().run("Nimages="+LIDCnImages+ ", startImg="+0+", filter="+LIDCimageExtension); setupImg(); // sets ptNodules == all nodules of interest for this patient/study initPtNodules(); String shortPtID = studyDirAt.substring(studyDirAt.lastIndexOf(".")+1); IJ.log(" study "+studyDirAt+" #nods "+ptNodules.length+" indexAt = "+l+"/"+NtrainingNods); for (int i=0; i

candidateSep

public float candidateSep(Point3D A,
                          NoduleCandidate B)

NCCCoptRadii

public void NCCCoptRadii(int candStart,
                         int candEnd,
                         int iter)

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

NCCCoptLoc

public void NCCCoptLoc(int candStart,
                       int candEnd)

calcKall

public float[][][][] calcKall(float radius,
                              float wpadding,
                              float dscale,
                              float wscale,
                              float hscale)

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. // and check for a grid of 3x5x5 pixels around current candidate location float topCorr = -1f; for (float dd = -0.4f; dd<=0.4f; dd+= 0.2f) for (float ww = -0.4f; ww<=0.4f; ww+= 0.2f) for (float hh = -0.4f; hh<=0.4f; hh+= 0.2f) { kshift = MathII.sphericalKernel(radAt, padAt, sliceThickness, mmPerPixelX, mmPerPixelY, dd,ww,hh); corrAll = ImgProc.aStatsCorrCirc(origimg, kshift, 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; if (bestFitLoc3D.value > topCorr) { topCorr = bestFitLoc3D.value; //** 1/31/11 not sure it should be +ii or -ii bestFitLoc = new NoduleCandidate(candidates[c].patientID, bestFitLoc3D.x, bestFitLoc3D.y, bestFitLoc3D.z, radAt, padAt, topCorr); } } // end shifts loop IJ.log(" best loc combo for cand "+candAt+": "+bestFitLoc); return bestFitLoc; } // end NCCCtestLoc

calcKall

public float[][][][] calcKall(float radius,
                              float wpadding,
                              float dscale,
                              float wscale,
                              float hscale,
                              float shiftd,
                              float shiftw,
                              float shifth)

kernelHitsChestWall

public boolean kernelHitsChestWall(NoduleCandidate c,
                                   float[][][] A)

addWall2Template

public float[][][] addWall2Template(float[][][] A,
                                    NoduleCandidate cand,
                                    float dilateSize)

addWall2Template

public float[][][] addWall2Template(float[][][] A,
                                    float k,
                                    float i,
                                    float j,
                                    float dilateSize)

addWall2Template

public float[][][][] addWall2Template(float[][][][] A,
                                      NoduleCandidate cand,
                                      float dilateSize)

addWall2Template

public float[][][][] addWall2Template(float[][][][] A,
                                      float k,
                                      float i,
                                      float j,
                                      float dilateSize)

redisplay

protected void redisplay()

Overrides:

redisplay in class ImageReviewer

initPtNodules

public void initPtNodules()

setupImg

public void setupImg()

Overrides:

setupImg in class ImageReviewer

getObjectMask

public void getObjectMask()

getLungMask

public void getLungMask()

toString

public java.lang.String toString()

Overrides:

toString in class ImageReviewer