woSource

Class AirwaySegm

java.lang.Object

woSource.ScreenSelectorClass

woSource.ImageReviewer

woSource.VesselSegm

woSource.AirwaySegm

All Implemented Interfaces:

ij.plugin.PlugIn

public class AirwaySegm
extends VesselSegm
implements ij.plugin.PlugIn

AirwaySegm by W. O'Dell 7/3/2013 - present
this uses much of the same code as the vessel segmentation program,
this is set up to run on unmasked CT dicom images of the chest.

About AirwayTrunk Segmentation...
This permits one to segment the airways (trachea, bronchi) from amongst the heart, ascending aorta and other structures in the medistinum, starting with a single seed location. Stores in objectMask

Field Summary

Fields

Modifier and Type	Field and Description
protected int	adjustedMax
int	autoRunButtonAt
protected int	bodyThresh
boolean	disableTraversal
boolean	enableCrop
protected float	ErosionRadius
boolean	isWoodSample
protected Rectangle3D	lungRect
protected int	maxthresh

Fields inherited from class woSource.VesselSegm

adjustedDiff, adjustedMin, airwayMask, autoRun, badAngleThresh, bigVesselBrightness, bodyRect, branchRadRatioThresh, closingOpSize, connTissueMask, didBodyCrop, didVesselCrop, distAd, havePulmTrunkMask, imagemax, imagemin, leftAtriumMask, leftAtriumSeedx, leftAtriumSeedy, leftAtriumSeedz, loopLocs, masksWereSaved, maxDiff, maxVoxelCount, mediastinumMask, minthresh, name_ext, nLoopPts, nOrphanedBranches, orphanedBranches, outputdir, parRadRatioThresh, pulmTrunkMask, seedVoxelValue, seedx, seedy, seedz, showDistAd, skelAd, slash, terminateOnSegmClose, threshAd, trunkMaxThresh, trunkMinThresh, trunkSeedx, trunkSeedy, trunkSeedz, trunkSkelStartPt, useDistanceTransform, vesselRect

Fields inherited from class woSource.ImageReviewer

working_canvas

Constructor Summary

Constructors

Constructor and Description
AirwaySegm()

Method Summary

Modifier and Type	Method and Description
void	customButFunc()
boolean	readInAirwayMaskFiles()
void	run(java.lang.String arg) This method is called when the plugin is loaded.
void	run(java.lang.String arg, ij.ImagePlus passedimp)
protected void	updateThreshold()

Methods inherited from class woSource.VesselSegm

AddLoopLocIfUnique, addOrphanedBranchLastPt, addOrphanedBranchPt, adjustBranchRadii, areBranchesPaired, areBranchesPaired, areRadiiMatched, areRadiiMatched, backTraceToMostOffendingBranch, backTraceToMostOffendingBranch, checkRemoveHyperskelPair, create3BrTestTree, create3DcrossingTestTree, createCrossingCylSimImage, createCylinderTestSimImage, createHyperSkelPair, createHyperSkelPair, cropToRect, DeleteLoopLoc, deleteOrphanedBranchPt, deleteTopOrphanedBranchPt, deleteTree, Draw, Draw, Draw, Draw, extendBranchEnds, findClosestSkeletonPt, findClosestSkeletonPt, findSkeletonTop, findSkeletonTop, findSkeletonTopTry, findSkeletonTopTry, findSkeletonTopTry, findSkeletonTopTry, forwardTraceToLargestBranch, forwardTraceToLargeTerminusBranch, forwardTraceToTreeTop, get2ndHyperSkelPairIndex, get2ndHyperSkelPairIndex, getChild1FrontVec, getChild1Index, getChild2FrontVec, getChild2Index, getChildrenBifurAngle, getFalse2DConnectionScore, getFalseLadderConnectionScore, getHyperSkelPairIndex, getHyperSkelPairIndex, getHyperskelPairPt, getHyperskelPairPt, getHyperskelPairPt, getLargestChildRadius, getLargestParentSiblingRadius, getLengthHistogram, getLoopedLocIndexForFromBr, getLoopedLocIndexForToBr, getOrphanedBranchOfTopPt, getPairNCCC, getPairTrimmedNCCC, getRadiusHistogram, getSepAngle, getSepAngle, getSiblingBifurAngle, getSiblingFrontVec, getSimImage, getSimImage, getTopLocIndex, getTreeBranchLabels, getTrimmedBranchEndVec, getTrimmedBranchFrontVec, getTrimmedBranchLength, getTrimmedBranchRadius, getTrimmedBranchRadius, handleFailedBranchRepair, hasMultipleLoopPairings, initialTraceAlongBranch, isAhyperSkelPt, isAhyperSkelPt, isALoopedFromLoc, isALoopedToLoc, isAtopLoc, isPointInAnyTree, readInOrComputeAirwayMask, readInOrComputeConnTissMask, readInOrComputeLungVolMask, readInOrComputePTLAmasks, readInPTLAmasks, ReadSimTreeParams, reallocateLoopedBranchesChildren, reallocateLoopLoc, repairBranchConnection, repairFalse2DConnection, repairFalseLadderConnection, repairLoopLocs, rmConnTissue, setPointRadii, setupMIPs, showBiggestTree, showCenterlinePts, shuffleLoopLocs, spaceWindowsOnScreen, splitTreeAtConnection, traceCenterline, traceCenterlines, traverseToFindTreeTop, trimBranchEndPts, trimSmoothEndPts, trimTreeStubs, updateMIPs, updateMIPs, updateMIPs, writeAllTreesSTL, writeBiggestTreeParams, writeBiggestTreeParams

Methods inherited from class woSource.ImageReviewer

adjustCurSlice, cropToObjectROI, customChoiceFunc, findClosestMark, get3Dview, get3DviewOfmark, getObjectMaskFromFiles, getObjectMaskFromFiles, getPtInputDirInfo, redisplay, 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

bodyThresh

protected int bodyThresh

maxthresh

protected int maxthresh

adjustedMax

protected int adjustedMax

lungRect

protected Rectangle3D lungRect

ErosionRadius

protected float ErosionRadius

isWoodSample

public boolean isWoodSample

disableTraversal

public boolean disableTraversal

enableCrop

public boolean enableCrop

autoRunButtonAt

public int autoRunButtonAt

Constructor Detail

AirwaySegm

public AirwaySegm()

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 VesselSegm

run

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

Overrides:

run in class VesselSegm

customButFunc

public void customButFunc()

Overrides:

customButFunc in class VesselSegm

updateThreshold

protected void updateThreshold()

Overrides:

updateThreshold in class VesselSegm

readInAirwayMaskFiles

public boolean readInAirwayMaskFiles()