HeartSegm (WOImageJ API)

java.lang.Object
- woSource.ScreenSelectorClass
- - woSource.ImageReviewer
  - - woSource.InteractiveSnake
    - - woSource.HeartSegm

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class HeartSegm
extends InteractiveSnake
implements ij.plugin.PlugIn
```
2/2/2015 WO need place where I try to read in the existing tag points. Workflow conerns: can't do tags until both contours are done, for all time frames. If you later adjust a contour then may need to clip or redefine the tag ends. May need way to increment/decrement tag indices on a single slice (hopefully not). After doing all contours maybe have button to do all tags.

Nested Class Summary
- Nested classes/interfaces inherited from class woSource.InteractiveSnake
  InteractiveSnake.Candidates, InteractiveSnake.SmoothSnake, InteractiveSnake.Snake, InteractiveSnake.SnakeStack

Field Summary

Fields
Modifier and Type	Field and Description
`protected float`	`con_ptSep`
`protected ContourFit`	`confit`
`InteractiveSnake.SnakeStack[][][]`	`conSnakeStacks`
`protected float[][][][]`	`contourPts`
`protected boolean`	`contoursOnly`
`protected int`	`curEndoEpi`
`protected int`	`curMyoIntensity`
`protected int`	`curSeries`
`protected int`	`curSlice`
`protected int`	`curTime`
`protected boolean[]`	`didAllCons`
`protected boolean`	`doingConsVsTags`
`protected java.lang.String[]`	`endepichoices`
`protected int`	`firstSAconIndex`
`Image3Dinfo[]`	`heartMR3Dinfo`
`protected ImageRegistrationPS`	`imreg`
`protected boolean[]`	`isLA`
`protected ij.gui.TruncatedEllipseRoi[]`	`LAselectedRoi`
`protected int`	`maxImgHeight`
`protected int`	`maxImgWidth`
`protected int`	`maxSlices`
`protected int`	`maxTimes`
`protected int[][]`	`nConPts`
`protected int`	`nProcessTimes`
`protected int`	`nSeries`
`protected int[]`	`nSlices`
`protected java.lang.String`	`patientDir`
`protected java.lang.String`	`patientOutputDir`
`protected int[]`	`PSfitOrder`
`protected Point3Dviewer`	`ptviewer`
`protected ij.gui.OvalRoi[]`	`SAselectedRoi`
`protected SeriesImagesClass[]`	`seriesImages`
`protected java.lang.String[]`	`SeriesNames`
`protected boolean`	`showingTagsVsFilled`
`protected SimTagImageInfo[]`	`simTagInfo`
`protected java.lang.String[][]`	`SliceNames`
`protected float[][]`	`tagBMfitCoeffs`
`protected float[][][]`	`tagPSfitCoeffs`
`protected java.awt.Rectangle[]`	`tagSearchRect`

Fields inherited from class woSource.InteractiveSnake
absGradient, cur_ptSep, cur_ptShift, curEnergy_Bend, curEnergy_Pressure, curEnergy_Stretch, DoFullyManual, enableCreateMaskSaveAsDicom, filename_addon, gradientIn, gradientOut, gradientType, Label, origSelectedRoi, ProhibitInwardPoints, runAsStandAlone, saveWindows, showEdgeImg, ShowLabels, snakeAd, snakegd, snakeptviewer, snakeStack, useAdditionalDrawingAD

Fields inherited from class woSource.ImageReviewer
working_canvas

Constructor Summary

Constructors
Constructor and Description

HeartSegm()

Constructors
Constructor and Description
`HeartSegm()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`short[][]`	`computeEdgeImage(byte[][] A)`
`short[][][]`	`computeEdgeImage(byte[][][] A)`
`short[][]`	`computeEdgeImage(short[][] A)`
`short[][][]`	`computeEdgeImage(short[][][] A)`
`void`	`convertConSnakePtsToArray()`
`boolean`	`didAllCurSeriesCons()`
`boolean`	`didAllSeriesCons(int seriesAt)`
`byte[][][]`	`fillInTags(byte[][][] A, boolean is45, float tagWidth)`
`byte[][]`	`fillInTags(byte[][] A, boolean is45, float tagWidth)`
`short[][][]`	`fillInTags(short[][][] A, boolean is45, float tagWidth)`
`short[][]`	`fillInTags(short[][] A, boolean is45, float tagWidth)`
`protected boolean`	`getHeartLAparams()`
`java.lang.String`	`getTagFilenameAddon(int tagat, int tfr)`
`void`	`GetTagParams(short[][] shortImg, int seriesAt)`
`void`	`GetTagParams(short[][] shortImg, int seriesAt, float initGuessAngle, float initGuessSpacing, float initGuessWidth)`
`byte[][]`	`getTestTagImg(byte[][] tagimg, float normangle, float tagspacing, float tagwidth, float tagoffset)`
`void`	`init(ij.ImagePlus passedimp)` snakestack == null is flag for interactiveSnake running as a stand-alone program
`void`	`initSnackStacks()`
`float[]`	`optOver2Params(short[][] selectedOrigImg, float fixedAngle, float tagSpacing, float fixedWidth, float tagOffset)`
`float[]`	`optOver3Params(short[][] selectedOrigImg, float fixedAngle, float tagSpacing, float tagWidth, float tagOffset)`
`float[]`	`optOver4Params(short[][] selectedOrigImg, float tagAngle, float tagSpacing, float tagWidth, float tagOffset)`
`void`	`optTagWarp(int timeAt)`
`void`	`readIn_allImages()`
`protected boolean`	`readInAllHeartLAinfo()`
`void`	`readInAllImagesAtTime(int timeAt)`
`boolean`	`readStudyInfo()`
`void`	`refreshScreen()`
`void`	`resetwidgets()`
`void`	`run(ij.ImagePlus passedimp)`
`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`	`setNewEndoEpi()`
`void`	`setNewSeries()`
`void`	`setNewSlice()`
`void`	`setNewTime()`
`void`	`showAbout()`
`void`	`sortFilesIntoSliceFolders()`
`void`	`spaceWindowsOnScreen()`
`void`	`syncCurrentStack()`
`void`	`updateSnakeStacksForNewSlice(int curser, int cursl, ArrayDisplay curAd)`
`void`	`veryFirstReadInAllImages()`
`boolean`	`writeAllHeartLAinfo()`
`boolean`	`writeStudyInfo()`

Methods inherited from class woSource.InteractiveSnake
CreateMask, InitSnakeDisplay, InitSnakeDisplay, setFilename_addon, toString, UpdateAttributes, UpdateScreen, UpdateSelection

Methods inherited from class woSource.ImageReviewer
adjustCurSlice, cropToObjectROI, customButFunc, customChoiceFunc, findClosestMark, get3Dview, get3DviewOfmark, getObjectMaskFromFiles, getObjectMaskFromFiles, getPtInputDirInfo, redisplay, runGUI, setGUIWinLevelWidgets, setNewStudy, setupImg, setupImg, setupImg, setupImg, updateMarkingPanel, 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

endepichoices

protected java.lang.String[] endepichoices

nSeries
```
protected int nSeries
```

maxImgWidth
```
protected int maxImgWidth
```

maxImgHeight
```
protected int maxImgHeight
```

isLA
```
protected boolean[] isLA
```

SeriesNames

protected java.lang.String[] SeriesNames

SliceNames

protected java.lang.String[][] SliceNames

heartMR3Dinfo
```
public Image3Dinfo[] heartMR3Dinfo
```

seriesImages

protected SeriesImagesClass[] seriesImages

curSeries
```
protected int curSeries
```

curSlice
```
protected int curSlice
```

maxSlices
```
protected int maxSlices
```

curEndoEpi
```
protected int curEndoEpi
```

curMyoIntensity
```
protected int curMyoIntensity
```

curTime
```
protected int curTime
```

maxTimes
```
protected int maxTimes
```

nSlices
```
protected int[] nSlices
```

nProcessTimes
```
protected int nProcessTimes
```

contoursOnly
```
protected boolean contoursOnly
```

conSnakeStacks

public InteractiveSnake.SnakeStack[][][] conSnakeStacks

SAselectedRoi

protected ij.gui.OvalRoi[] SAselectedRoi

LAselectedRoi

protected ij.gui.TruncatedEllipseRoi[] LAselectedRoi

patientDir
```
protected java.lang.String patientDir
```

patientOutputDir

protected java.lang.String patientOutputDir

firstSAconIndex
```
protected int firstSAconIndex
```

simTagInfo
```
protected SimTagImageInfo[] simTagInfo
```

tagSearchRect

protected java.awt.Rectangle[] tagSearchRect

imreg
```
protected ImageRegistrationPS imreg
```

tagBMfitCoeffs
```
protected float[][] tagBMfitCoeffs
```

tagPSfitCoeffs
```
protected float[][][] tagPSfitCoeffs
```

PSfitOrder
```
protected int[] PSfitOrder
```

con_ptSep
```
protected float con_ptSep
```

doingConsVsTags
```
protected boolean doingConsVsTags
```

showingTagsVsFilled
```
protected boolean showingTagsVsFilled
```

didAllCons
```
protected boolean[] didAllCons
```

ptviewer
```
protected Point3Dviewer ptviewer
```

confit
```
protected ContourFit confit
```

nConPts
```
protected int[][] nConPts
```

contourPts
```
protected float[][][][] contourPts
```

Constructor Detail
- HeartSegm
```
public HeartSegm()
```

Method Detail

showAbout
```
public void showAbout()
```
Overrides:

showAbout in class InteractiveSnake

init
```
public void init(ij.ImagePlus passedimp)
```
Description copied from class: InteractiveSnake

snakestack == null is flag for interactiveSnake running as a stand-alone program

Overrides:

init in class InteractiveSnake

didAllSeriesCons

public boolean didAllSeriesCons(int seriesAt)

didAllCurSeriesCons
```
public boolean didAllCurSeriesCons()
```

run

public void run(ij.ImagePlus passedimp)

Overrides:: run in class InteractiveSnake

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 InteractiveSnake

run

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

Overrides:: run in class InteractiveSnake

setNewSeries
```
public void setNewSeries()
```

setNewSlice
```
public void setNewSlice()
```
Overrides:

setNewSlice in class ImageReviewer

setNewEndoEpi
```
public void setNewEndoEpi()
```

setNewTime
```
public void setNewTime()
```

syncCurrentStack
```
public void syncCurrentStack()
```

updateSnakeStacksForNewSlice

public void updateSnakeStacksForNewSlice(int curser,
                                         int cursl,
                                         ArrayDisplay curAd)

computeEdgeImage
```
public short[][][] computeEdgeImage(byte[][][] A)
```
Overrides:

computeEdgeImage in class InteractiveSnake

computeEdgeImage

public short[][] computeEdgeImage(byte[][] A)

computeEdgeImage
```
public short[][][] computeEdgeImage(short[][][] A)
```
Overrides:

computeEdgeImage in class InteractiveSnake

computeEdgeImage

public short[][] computeEdgeImage(short[][] A)

readInAllImagesAtTime

public void readInAllImagesAtTime(int timeAt)

optTagWarp
```
public void optTagWarp(int timeAt)
```

writeAllHeartLAinfo
```
public boolean writeAllHeartLAinfo()
```

readInAllHeartLAinfo

protected boolean readInAllHeartLAinfo()

getHeartLAparams
```
protected boolean getHeartLAparams()
```

getTagFilenameAddon

public java.lang.String getTagFilenameAddon(int tagat,
                                            int tfr)

getTestTagImg

public byte[][] getTestTagImg(byte[][] tagimg,
                              float normangle,
                              float tagspacing,
                              float tagwidth,
                              float tagoffset)

optOver2Params

public float[] optOver2Params(short[][] selectedOrigImg,
                              float fixedAngle,
                              float tagSpacing,
                              float fixedWidth,
                              float tagOffset)

optOver3Params

public float[] optOver3Params(short[][] selectedOrigImg,
                              float fixedAngle,
                              float tagSpacing,
                              float tagWidth,
                              float tagOffset)

optOver4Params

public float[] optOver4Params(short[][] selectedOrigImg,
                              float tagAngle,
                              float tagSpacing,
                              float tagWidth,
                              float tagOffset)

GetTagParams

public void GetTagParams(short[][] shortImg,
                         int seriesAt)

GetTagParams

public void GetTagParams(short[][] shortImg,
                         int seriesAt,
                         float initGuessAngle,
                         float initGuessSpacing,
                         float initGuessWidth)

fillInTags

public byte[][] fillInTags(byte[][] A,
                           boolean is45,
                           float tagWidth)

fillInTags

public byte[][][] fillInTags(byte[][][] A,
                             boolean is45,
                             float tagWidth)

fillInTags

public short[][] fillInTags(short[][] A,
                            boolean is45,
                            float tagWidth)

fillInTags

public short[][][] fillInTags(short[][][] A,
                              boolean is45,
                              float tagWidth)

resetwidgets
```
public void resetwidgets()
```
Overrides:

resetwidgets in class ImageReviewer

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

spaceWindowsOnScreen in class InteractiveSnake

refreshScreen
```
public void refreshScreen()
```
Overrides:

refreshScreen in class InteractiveSnake

sortFilesIntoSliceFolders

public void sortFilesIntoSliceFolders()

veryFirstReadInAllImages

public void veryFirstReadInAllImages()

readIn_allImages
```
public void readIn_allImages()
```

initSnackStacks
```
public void initSnackStacks()
```

convertConSnakePtsToArray

public void convertConSnakePtsToArray()

writeStudyInfo
```
public boolean writeStudyInfo()
```

readStudyInfo

public boolean readStudyInfo()
                      throws java.io.IOException

Throws:: java.io.IOException

Class HeartSegm

Nested Class Summary

Nested classes/interfaces inherited from class woSource.InteractiveSnake

Field Summary

Fields inherited from class woSource.InteractiveSnake

Fields inherited from class woSource.ImageReviewer

Constructor Summary

Method Summary

Methods inherited from class woSource.InteractiveSnake

Methods inherited from class woSource.ImageReviewer

Methods inherited from class woSource.ScreenSelectorClass

Methods inherited from class java.lang.Object

Field Detail

endepichoices

nSeries

maxImgWidth

maxImgHeight

isLA

SeriesNames

SliceNames

heartMR3Dinfo

seriesImages

curSeries

curSlice

maxSlices

curEndoEpi

curMyoIntensity

curTime

maxTimes

nSlices

nProcessTimes

contoursOnly

conSnakeStacks

SAselectedRoi

LAselectedRoi

patientDir

patientOutputDir

firstSAconIndex

simTagInfo

tagSearchRect

imreg

tagBMfitCoeffs

tagPSfitCoeffs

PSfitOrder

con_ptSep

doingConsVsTags

showingTagsVsFilled

didAllCons

ptviewer

confit

nConPts

contourPts

Constructor Detail

HeartSegm

Method Detail

showAbout

init

didAllSeriesCons

didAllCurSeriesCons

run

run

run

setNewSeries

setNewSlice

setNewEndoEpi

setNewTime

syncCurrentStack

updateSnakeStacksForNewSlice

computeEdgeImage

computeEdgeImage

computeEdgeImage

computeEdgeImage

readInAllImagesAtTime

optTagWarp

writeAllHeartLAinfo

readInAllHeartLAinfo

getHeartLAparams

getTagFilenameAddon

getTestTagImg

optOver2Params