humanLungSegm (WOImageJ API)

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

All Implemented Interfaces:: ij.plugin.PlugIn

public class humanLungSegm
extends ImageReviewer
implements ij.plugin.PlugIn

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`alreadyBodyCropped`
`protected boolean`	`alreadyCropped`
`protected boolean`	`autoCropHilumVessels`
`protected float`	`bigVesselCloseOpRadius`
`protected Rectangle3D`	`bodyROI`
`protected short`	`bodyThresh`
`boolean`	`debugLungSegmen`
`boolean`	`debugSnakes`
`boolean`	`doManualLungSegm`
`boolean`	`doRunGUI`
`boolean`	`doSnakesOnPrevMasks`
`protected int`	`erodeDilateOpRad`
`boolean`	`havePulmTrunkMask`
`protected Rectangle3D`	`innerbodyROI`
`protected java.lang.String`	`inputdir`
`protected int`	`intestineErodDilRad`
`protected byte[][][]`	`leftLung`
`protected GenericRecallableDialog`	`lunggd`
`protected boolean[][][]`	`lungMask`
`protected byte[][][]`	`lungMaskByte`
`protected Rectangle3D`	`lungROI`
`protected boolean[][][]`	`pulmTrunkMask`
`protected ArrayDisplay`	`resultAd`
`protected byte[][][]`	`rightLung`
`protected boolean`	`ROIwasRead`
`protected int`	`startDepth`
`protected java.lang.String`	`targetNodsFile`

Fields inherited from class woSource.ImageReviewer
working_canvas

Constructor Summary

Constructors
Constructor and Description

humanLungSegm()

Constructors
Constructor and Description
`humanLungSegm()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`batchRunHLS()`
`void`	`customButFunc()`
`void`	`doManualLungSeg()`
`void`	`doSnakeLungSegm()`
`void`	`getLungMask(boolean readInJPGs)`
`protected void`	`redisplay()`
`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`	`showAbout()`
`void`	`spaceWindowsOnScreen()`
`void`	`splitHemiLungs()` ultimately sets the globally-defined leftLung and rightLung byte[][][] mask arrays \n Works on lungMaskByte and expects on start that lungs are black, outside body and body = white

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

doManualLungSegm
```
public boolean doManualLungSegm
```

debugSnakes
```
public boolean debugSnakes
```

debugLungSegmen
```
public boolean debugLungSegmen
```

doSnakesOnPrevMasks
```
public boolean doSnakesOnPrevMasks
```

havePulmTrunkMask
```
public boolean havePulmTrunkMask
```

lungMaskByte
```
protected byte[][][] lungMaskByte
```

leftLung
```
protected byte[][][] leftLung
```

rightLung
```
protected byte[][][] rightLung
```

lungMask
```
protected boolean[][][] lungMask
```

pulmTrunkMask
```
protected boolean[][][] pulmTrunkMask
```

targetNodsFile

protected java.lang.String targetNodsFile

bodyROI
```
protected Rectangle3D bodyROI
```

innerbodyROI
```
protected Rectangle3D innerbodyROI
```

lungROI
```
protected Rectangle3D lungROI
```

alreadyCropped
```
protected boolean alreadyCropped
```

alreadyBodyCropped
```
protected boolean alreadyBodyCropped
```

doRunGUI
```
public boolean doRunGUI
```

resultAd
```
protected ArrayDisplay resultAd
```

bodyThresh
```
protected short bodyThresh
```

intestineErodDilRad
```
protected int intestineErodDilRad
```

erodeDilateOpRad
```
protected int erodeDilateOpRad
```

autoCropHilumVessels
```
protected boolean autoCropHilumVessels
```

bigVesselCloseOpRadius
```
protected float bigVesselCloseOpRadius
```

lunggd

protected GenericRecallableDialog lunggd

startDepth
```
protected int startDepth
```

ROIwasRead
```
protected boolean ROIwasRead
```

inputdir
```
protected java.lang.String inputdir
```

Constructor Detail
- humanLungSegm
```
public humanLungSegm()
```

Method Detail
- showAbout
```
public void showAbout()
```
- 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
- redisplay
```
protected void redisplay()
```
  Overrides:
  
  redisplay in class ImageReviewer
- getLungMask
```
public void getLungMask(boolean readInJPGs)
```
- splitHemiLungs
```
public void splitHemiLungs()
```
  ultimately sets the globally-defined leftLung and rightLung byte[][][] mask arrays \n Works on lungMaskByte and expects on start that lungs are black, outside body and body = white
- doSnakeLungSegm
```
public void doSnakeLungSegm()
```
- doManualLungSeg
```
public void doManualLungSeg()
```
- batchRunHLS
```
public void batchRunHLS()
```
- spaceWindowsOnScreen
```
public void spaceWindowsOnScreen()
```
  Overrides:
  
  spaceWindowsOnScreen in class ImageReviewer

Class humanLungSegm

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

doManualLungSegm

debugSnakes

debugLungSegmen

doSnakesOnPrevMasks

havePulmTrunkMask

lungMaskByte

leftLung

rightLung

lungMask

pulmTrunkMask

targetNodsFile

bodyROI

innerbodyROI

lungROI

alreadyCropped

alreadyBodyCropped

doRunGUI

resultAd

bodyThresh

intestineErodDilRad

erodeDilateOpRad

autoCropHilumVessels

bigVesselCloseOpRadius

lunggd

startDepth

ROIwasRead

inputdir

Constructor Detail

humanLungSegm

Method Detail

showAbout

run

run

customButFunc

redisplay

getLungMask

splitHemiLungs

doSnakeLungSegm

doManualLungSeg

batchRunHLS

spaceWindowsOnScreen