woSource

Class ColonSegm

java.lang.Object

woSource.ScreenSelectorClass

woSource.ImageReviewer

woSource.VesselSegm

woSource.ColonSegm

All Implemented Interfaces:

ij.plugin.PlugIn

public class ColonSegm
extends VesselSegm
implements ij.plugin.PlugIn

Field Summary

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, 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
ColonSegm()

Method Summary

Modifier and Type	Method and Description
protected void	applyTaggedFecesThresh()
protected void	applyVertLineSegm()
protected void	cropToRect(Rectangle3D curRect)
void	customButFunc()
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	updateThresholds()

Methods inherited from class woSource.VesselSegm

AddLoopLocIfUnique, addOrphanedBranchLastPt, addOrphanedBranchPt, adjustBranchRadii, areBranchesPaired, areBranchesPaired, areRadiiMatched, areRadiiMatched, backTraceToMostOffendingBranch, backTraceToMostOffendingBranch, checkRemoveHyperskelPair, create3BrTestTree, create3DcrossingTestTree, createCrossingCylSimImage, createCylinderTestSimImage, createHyperSkelPair, createHyperSkelPair, 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, updateThreshold, 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

Constructor Detail

ColonSegm

public ColonSegm()

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

applyVertLineSegm

protected void applyVertLineSegm()

applyTaggedFecesThresh

protected void applyTaggedFecesThresh()

cropToRect

protected void cropToRect(Rectangle3D curRect)

Overrides:

cropToRect in class VesselSegm

updateThresholds

protected void updateThresholds()