PulmonaryTrunkSegm (WOImageJ API)

java.lang.Object
- woSource.ScreenSelectorClass
- - woSource.ImageReviewer
  - - woSource.PulmonaryTrunkSegm

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class PulmonaryTrunkSegm
extends ImageReviewer
implements ij.plugin.PlugIn
```
PulmonaryTrunkSegm 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, preferably with vascular contrast.
About PulmonaryTrunk Segmentation...
This permits one to segment the pulmonary trunk (lung inflow) and left artium and lung outflow from amongst the heart, ascending aorta and other structures in the medistinum, starting with a single seed location.
also generates and saves the connectiveTissueMask
1. Cropping to body.
2. call human lung segm if needed
3. Min Vessel threshold: limit search to pixels with value > threshold to exclude myocardium
4. Select seed point by double-clicking mouse over approximate vessel tree root.
5. perform successive erosions to indentify where the aorta is clipped off.
6. keep the pulmonary root FF result and dilate just that.
7. Save mask images.

Field Summary

Fields
Modifier and Type	Field and Description
`protected int`	`adjustedMax`
`protected int`	`adjustedMin`
`protected int`	`airBGThresh`
`protected int`	`airBGThresh_adjusted`
`protected int`	`ARSeedx`
`protected int`	`ARSeedy`
`protected int`	`ARSeedz`
`protected int`	`bodyThresh`
`protected boolean`	`didLungCrop`
`protected float[][][]`	`distMap`
`protected float`	`ErosionRadius`
`protected int`	`imagemax`
`protected int`	`imagemin`
`protected boolean[][][]`	`LAbodyMask`
`protected ArrayDisplay`	`LAmaskAd`
`protected int`	`LASeedx`
`protected int`	`LASeedy`
`protected int`	`LASeedz`
`protected VesselSegm`	`LAvesselsegm`
`protected Rectangle3D`	`lungRect`
`protected int`	`LVSeedx`
`protected int`	`LVSeedy`
`protected int`	`LVSeedz`
`protected boolean`	`masksWereSaved`
`int`	`maxthresh`
`int`	`minthresh`
`protected java.lang.String`	`name_ext`
`protected int`	`ntreeTops`
`protected java.lang.String`	`outputdir`
`protected boolean`	`PTLAmasksWereReadIn`
`protected int`	`ptSeedx`
`protected int`	`ptSeedy`
`protected int`	`ptSeedz`
`protected int`	`RVSeedx`
`protected int`	`RVSeedy`
`protected int`	`RVSeedz`
`protected boolean`	`saveConnTissMask`
`protected boolean`	`saveRVLVmasks`
`protected int`	`seedVoxelValue`
`protected java.lang.String`	`slash`
`protected ArrayDisplay`	`threshAd`
`protected Point3Dint[]`	`treeTops`
`protected int`	`upperConnThresh`
`protected VesselSegm`	`vesselsegm`

Fields inherited from class woSource.ImageReviewer
working_canvas

Constructor Summary

Constructors
Constructor and Description

PulmonaryTrunkSegm()

Constructors
Constructor and Description
`PulmonaryTrunkSegm()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`cropToRect(Rectangle3D curRect)`
`void`	`customButFunc()`
`void`	`doTraversal()`
`void`	`getWriteTreeSimImage(VesselTree treeAt)`
`void`	`getWriteTreeSTL(VesselTree treeAt)`
`void`	`hideAllDisplays()`
`boolean`	`readInOrComputeLungVolMask()`
`boolean`	`readPTdata(java.lang.String path)`
`void`	`reFillMasks(int thisThresh)`
`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`	`savePTdata()`
`void`	`sepByDistAllMasks()`
`void`	`setupMIPs(byte[][][] maskedImg, byte[][][] labelsImg)`
`void`	`showAllDisplays()`
`void`	`spaceWindowsOnScreen()`
`void`	`updateMIPs(boolean[][][] mask)`
`void`	`updateMIPs(byte[][][] maskedImg)`
`void`	`updateMIPs(byte[][][] maskedImg, byte[][][] labelsImg)`
`protected void`	`updateThreshold()`

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
```

upperConnThresh
```
protected int upperConnThresh
```

airBGThresh
```
protected int airBGThresh
```

minthresh
```
public int minthresh
```

maxthresh
```
public int maxthresh
```

imagemax
```
protected int imagemax
```

imagemin
```
protected int imagemin
```

adjustedMin
```
protected int adjustedMin
```

adjustedMax
```
protected int adjustedMax
```

airBGThresh_adjusted
```
protected int airBGThresh_adjusted
```

ErosionRadius
```
protected float ErosionRadius
```

outputdir
```
protected java.lang.String outputdir
```

slash
```
protected java.lang.String slash
```

name_ext
```
protected java.lang.String name_ext
```

threshAd
```
protected ArrayDisplay threshAd
```

LAmaskAd
```
protected ArrayDisplay LAmaskAd
```

ptSeedx
```
protected int ptSeedx
```

ptSeedy
```
protected int ptSeedy
```

ptSeedz
```
protected int ptSeedz
```

LASeedx
```
protected int LASeedx
```

LASeedy
```
protected int LASeedy
```

LASeedz
```
protected int LASeedz
```

ARSeedx
```
protected int ARSeedx
```

ARSeedy
```
protected int ARSeedy
```

ARSeedz
```
protected int ARSeedz
```

LVSeedx
```
protected int LVSeedx
```

LVSeedy
```
protected int LVSeedy
```

LVSeedz
```
protected int LVSeedz
```

RVSeedx
```
protected int RVSeedx
```

RVSeedy
```
protected int RVSeedy
```

RVSeedz
```
protected int RVSeedz
```

seedVoxelValue
```
protected int seedVoxelValue
```

treeTops
```
protected Point3Dint[] treeTops
```

ntreeTops
```
protected int ntreeTops
```

LAbodyMask
```
protected boolean[][][] LAbodyMask
```

distMap
```
protected float[][][] distMap
```

lungRect
```
protected Rectangle3D lungRect
```

PTLAmasksWereReadIn
```
protected boolean PTLAmasksWereReadIn
```

saveRVLVmasks
```
protected boolean saveRVLVmasks
```

saveConnTissMask
```
protected boolean saveConnTissMask
```

masksWereSaved
```
protected boolean masksWereSaved
```

didLungCrop
```
protected boolean didLungCrop
```

vesselsegm
```
protected VesselSegm vesselsegm
```

LAvesselsegm
```
protected VesselSegm LAvesselsegm
```

Constructor Detail
- PulmonaryTrunkSegm
```
public PulmonaryTrunkSegm()
```

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

customButFunc
```
public void customButFunc()
```
Overrides:

customButFunc in class ImageReviewer

sepByDistAllMasks
```
public void sepByDistAllMasks()
```

reFillMasks

public void reFillMasks(int thisThresh)

setupMIPs

public void setupMIPs(byte[][][] maskedImg,
                      byte[][][] labelsImg)

updateMIPs

public void updateMIPs(boolean[][][] mask)

updateMIPs

public void updateMIPs(byte[][][] maskedImg)

updateMIPs

public void updateMIPs(byte[][][] maskedImg,
                       byte[][][] labelsImg)

hideAllDisplays
```
public void hideAllDisplays()
```

showAllDisplays
```
public void showAllDisplays()
```

spaceWindowsOnScreen
```
public void spaceWindowsOnScreen()
```
Overrides:

spaceWindowsOnScreen in class ImageReviewer

updateThreshold
```
protected void updateThreshold()
```

cropToRect

protected void cropToRect(Rectangle3D curRect)

readInOrComputeLungVolMask

public boolean readInOrComputeLungVolMask()

savePTdata
```
public void savePTdata()
```

readPTdata

public boolean readPTdata(java.lang.String path)

getWriteTreeSimImage

public void getWriteTreeSimImage(VesselTree treeAt)

getWriteTreeSTL

public void getWriteTreeSTL(VesselTree treeAt)

doTraversal
```
public void doTraversal()
```

Class PulmonaryTrunkSegm

Field Summary

Fields inherited from class woSource.ImageReviewer

Constructor Summary

Method Summary

Methods inherited from class woSource.ImageReviewer

Methods inherited from class woSource.ScreenSelectorClass

Methods inherited from class java.lang.Object

Field Detail

bodyThresh

upperConnThresh

airBGThresh

minthresh

maxthresh

imagemax

imagemin

adjustedMin

adjustedMax

airBGThresh_adjusted

ErosionRadius

outputdir

slash

name_ext

threshAd

LAmaskAd

ptSeedx

ptSeedy

ptSeedz

LASeedx

LASeedy

LASeedz

ARSeedx

ARSeedy

ARSeedz

LVSeedx

LVSeedy

LVSeedz

RVSeedx

RVSeedy

RVSeedz

seedVoxelValue

treeTops

ntreeTops

LAbodyMask

distMap

lungRect

PTLAmasksWereReadIn

saveRVLVmasks

saveConnTissMask

masksWereSaved

didLungCrop

vesselsegm

LAvesselsegm

Constructor Detail

PulmonaryTrunkSegm

Method Detail

run

run

customButFunc

sepByDistAllMasks

reFillMasks

setupMIPs

updateMIPs

updateMIPs

updateMIPs

hideAllDisplays

showAllDisplays

spaceWindowsOnScreen

updateThreshold

cropToRect

readInOrComputeLungVolMask

savePTdata

readPTdata

getWriteTreeSimImage

getWriteTreeSTL

doTraversal