woSource

Class noduleDetectionModule

java.lang.Object

woSource.ScreenSelectorClass

woSource.ImageReviewer

woSource.noduleDetectionModule

All Implemented Interfaces:

ij.plugin.PlugIn

public class noduleDetectionModule
extends ImageReviewer
implements ij.plugin.PlugIn

WO 7/31/2012, This is the version of NoduleDetection that runs when the user selects nodule detection from the Main Menu -> Process tab. The original NoduleDetection.java is not used.
I started by copying noduleDetection.java into noduleDetectionModule.java where the original did lung segmentation, in batch mode on the LIDC data, and then optimized the nodule detection part.
I want here just the nodule detection stuff and expect in the future that noduleDetection.java will utilize the improved and modular humanLungSegm.java code.
This assumes that objectMask is set for nodule search region

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	noduleDetectionModule.myOptThread
class	noduleDetectionModule.NodDetThread

Field Summary

Fields

Modifier and Type	Field and Description
protected ArrayDisplay	corrAd
protected boolean	doEdgePtsOnly
protected boolean[][][]	edgePtsImage
protected int	fineThresh
protected int	firstPassThresh
protected boolean	haveLungVolMaskImgs
protected float[]	krads
protected java.lang.String	name_ext
protected int	Nextrema
protected GenericRecallableDialog	prepgd
protected ArrayDisplay	templateAd
protected boolean[][][]	thinnedEdgePts

Fields inherited from class woSource.ImageReviewer

working_canvas

Constructor Summary

Constructors

Constructor and Description
noduleDetectionModule()

Method Summary

Modifier and Type	Method and Description
float[][][][]	addHalfBlock4ptNormal(float[][][][] kshifts, float[] vecNorm)
void	applySelectionTemplates()
void	applyTemplates()
NoduleCandidate[]	applyTemplates4Selections(int sliceStart, int sliceEnd)
NoduleCandidate[]	applyTemplates4Selections(int sliceStart, int sliceEnd, int threadIndex)
float[][][][]	calcKall(float radius, float wpadding, float dscale, float wscale, float hscale)
float[][][][]	calcKall(float radius, float wpadding, float dscale, float wscale, float hscale, float shiftd, float shiftw, float shifth)
float[][][][]	createTemplates(float radius, float padding, float slThick, float mmx, float mmy)
protected void	cropToRect(Rectangle3D curRect)
void	customButFunc()
void	doNCCCopt(java.lang.String optType)
float	getPadding(float radius)
void	NCCCoptLoc(int candStart, int candEnd)
void	NCCCoptPadding(int candStart, int candEnd)
void	NCCCoptRadii(int candStart, int candEnd, int iter)
void	optimizeOverCands()
void	overlayBestCandTemplate()
protected void	redisplay()
protected NoduleCandidate[]	rmRedundantPts(NoduleCandidate[] A, float sepThresh, float wscale, float hscale, float dscale)
void	run(java.lang.String arg) This method is called when the plugin is loaded.
void	run(java.lang.String arg, ij.ImagePlus passedimp)
void	spaceWindowsOnScreen()

Methods inherited from class woSource.ImageReviewer

adjustCurSlice, cropToObjectROI, customChoiceFunc, findClosestMark, get3Dview, get3DviewOfmark, getObjectMaskFromFiles, getObjectMaskFromFiles, getPtInputDirInfo, resetwidgets, runGUI, setGUIWinLevelWidgets, setNewSlice, setNewStudy, setupImg, setupImg, setupImg, setupImg, toString, updateMarkingPanel, UpdateScreen, 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

Field Detail

corrAd

protected ArrayDisplay corrAd

templateAd

protected ArrayDisplay templateAd

prepgd

protected GenericRecallableDialog prepgd

firstPassThresh

protected int firstPassThresh

fineThresh

protected int fineThresh

Nextrema

protected int Nextrema

krads

protected float[] krads

edgePtsImage

protected boolean[][][] edgePtsImage

thinnedEdgePts

protected boolean[][][] thinnedEdgePts

doEdgePtsOnly

protected boolean doEdgePtsOnly

name_ext

protected java.lang.String name_ext

haveLungVolMaskImgs

protected boolean haveLungVolMaskImgs

Constructor Detail

noduleDetectionModule

public noduleDetectionModule()

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

run

public void run(java.lang.String arg,
                ij.ImagePlus passedimp)

Overrides:

run in class ImageReviewer

spaceWindowsOnScreen

public void spaceWindowsOnScreen()

Overrides:

spaceWindowsOnScreen in class ImageReviewer

customButFunc

public void customButFunc()

Overrides:

customButFunc in class ImageReviewer

cropToRect

protected void cropToRect(Rectangle3D curRect)

createTemplates

public float[][][][] createTemplates(float radius,
                                     float padding,
                                     float slThick,
                                     float mmx,
                                     float mmy)

addHalfBlock4ptNormal

public float[][][][] addHalfBlock4ptNormal(float[][][][] kshifts,
                                           float[] vecNorm)

applyTemplates

public void applyTemplates()

applySelectionTemplates

public void applySelectionTemplates()

overlayBestCandTemplate

public void overlayBestCandTemplate()

getPadding

public float getPadding(float radius)

applyTemplates4Selections

public NoduleCandidate[] applyTemplates4Selections(int sliceStart,
                                                   int sliceEnd)

applyTemplates4Selections

public NoduleCandidate[] applyTemplates4Selections(int sliceStart,
                                                   int sliceEnd,
                                                   int threadIndex)

optimizeOverCands

public void optimizeOverCands()

NCCCoptRadii

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

doNCCCopt

public void doNCCCopt(java.lang.String optType)

NCCCoptLoc

public void NCCCoptLoc(int candStart,
                       int candEnd)

NCCCoptPadding

public void NCCCoptPadding(int candStart,
                           int candEnd)

redisplay

protected void redisplay()

Overrides:

redisplay in class ImageReviewer

rmRedundantPts

protected NoduleCandidate[] rmRedundantPts(NoduleCandidate[] A,
                                           float sepThresh,
                                           float wscale,
                                           float hscale,
                                           float dscale)

calcKall

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

calcKall

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