SegmentationModel (Deforming Mesh 0.9.4-SNAPSHOT API)

java.lang.Object
- deformablemesh.SegmentationModel

public class SegmentationModel
extends Object

Field Summary

Fields
Modifier and Type Field and Description

ImageEnergyType energyType

Fields
Modifier and Type	Field and Description
`ImageEnergyType`	`energyType`

Constructor Summary

Constructors
Constructor and Description

SegmentationModel()

Constructors
Constructor and Description
`SegmentationModel()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addFrameListener(FrameListener listener)`
`void`	`addMeshListener(FrameListener listener)`
`void`	`addMeshToTrack(int f, DeformableMesh3D mesh, Track track)`
`void`	`addMeshTrack(Track track)`
`void`	`calculateActinIntensity()`
`void`	`calculateInterfaceLineScan(int index, List<Track> tracks)`
`void`	`calculateInterfaceLineScan(Track track)`
`void`	`calculateInterfaceLineScans()`
`void`	`calculateLineScans()`
`void`	`calculateVolume()`
`void`	`createBinaryImage()`
`void`	`createEnergyImage()`
`void`	`createMosaicImage()`
`DeformableMesh3D`	`createSubMesh(DeformableMesh3D mesh, Set<Triangle3D> triangles)`
`void`	`deformMesh(DeformableMesh3D mesh)` Deforms the provided mesh using the prepared energies and values.
`void`	`deformMesh(int count)`
`void`	`deformMeshes(List<DeformableMesh3D> meshes, int steps)` A generic method for deforming all of the meshes provided.
`void`	`exportAsPly(File f)`
`void`	`exportAsStl(File f)`
`void`	`exportAsWireframeStl(File f)`
`void`	`externalEnergies()`
`ExternalEnergy`	`generateImageEnergy(DeformableMesh3D mesh)`
`List<Track>`	`getAllTracks()`
`double`	`getAlpha()`
`double`	`getBeta()`
`Box3D`	`getBounds()`
`double`	`getCortexThickness()`
`int`	`getCurrentFrame()`
`long`	`getDeformationCount()`
`int`	`getDivisions()`
`List<ExternalEnergy>`	`getExternalEnergies()` returns a list of all the external energies, except 'ring energy' affecting the currently selected mesh.
`List<ExternalEnergy>`	`getExternalEnergies(DeformableMesh3D selectedMesh)`
`double`	`getGamma()`
`double`	`getImageWeight()`
`File`	`getLastSavedFile()`
`int`	`getNChannels()`
`double`	`getNormalizeWeight()`
`int[]`	`getOriginalStackDimensions()`
`double`	`getPressure()`
`RingController`	`getRingController()`
`DeformableMesh3D`	`getSelectedMesh(int frame)`
`Track`	`getSelectedTrack()`
`String`	`getShortImageName()`
`double`	`getStericNeighborWeight()`
`double[]`	`getSurfaceOffsets()`
`double`	`getZToYScale()`
`boolean`	`hasNextFrame()`
`boolean`	`hasSelectedMesh()`
`boolean`	`isHardBoundaries()`
`void`	`load3DFurrows(File f)`
`void`	`measureAllVolumes()`
`void`	`measureSelectedMesh()`
`void`	`nextFrame()`
`void`	`notifyMeshListeners()`
`void`	`previousFrame()`
`void`	`removeFrameListener(FrameListener listener)`
`void`	`removeMeshFromTrack(int frame, DeformableMesh3D mesh, Track track)`
`void`	`removeMeshListener(FrameListener listener)`
`void`	`removeMeshTrack(Track track)`
`void`	`saveFurrows(File f)`
`void`	`saveMeshes(File f)`
`void`	`selectMeshTrack(Track track)`
`void`	`selectNextTrack()`
`void`	`selectPreviousTrack()`
`void`	`selectTrackWithMesh(DeformableMesh3D mesh)`
`void`	`setAlpha(double alpha)`
`void`	`setBeta(double beta)`
`void`	`setCortexThickness(double d)`
`void`	`setDivisions(int i)`
`void`	`setFrame(int i)`
`void`	`setGamma(double gamma)`
`void`	`setHardBoundaries(boolean hardBoundaries)`
`void`	`setImageEnergyType(ImageEnergyType i)` The energy type will be used to decide which image energy is add during deformations.
`void`	`setLastSavedFile(File lastSavedFile)`
`void`	`setMeshes(List<Track> meshes)`
`void`	`setNormalizerWeight(double d)`
`void`	`setOriginalPlus(ij.ImagePlus plus)` Sets the backing image plus, defaulting the channel to 0 and the frame to the current frame.
`void`	`setOriginalPlus(ij.ImagePlus plus, int channel)` Sets the current backing image to the provided image at the selected channel and the current frame.
`void`	`setOriginalPlus(ij.ImagePlus plus, int frame, int channel)`
`void`	`setPressure(double p)`
`void`	`setRingController(RingController ringController)`
`void`	`setStericNeighborWeight(double d)`
`void`	`setWeight(double d)`
`void`	`showCurvature()`
`void`	`showFurrowValues()` Creates a text window with the current furrow values scaled to the image units.
`void`	`showStress()`
`Track`	`startEmptyTrack()` Starts a track that is not used but has a name unique to the existing tracks.
`Track`	`startMeshTrack(int frame, DeformableMesh3D freshMesh)`
`void`	`stopRunning()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- energyType
```
public ImageEnergyType energyType
```

Constructor Detail
- SegmentationModel
```
public SegmentationModel()
```

Method Detail

getDeformationCount
```
public long getDeformationCount()
```

deformMesh
```
public void deformMesh(int count)
```

deformMeshes

public void deformMeshes(List<DeformableMesh3D> meshes,
                         int steps)

A generic method for deforming all of the meshes provided.

Parameters:: meshes -

deformMesh
```
public void deformMesh(DeformableMesh3D mesh)
```
Deforms the provided mesh using the prepared energies and values. Will reshape each iteration.

Parameters:

mesh -

stopRunning
```
public void stopRunning()
```

setGamma
```
public void setGamma(double gamma)
```

setAlpha
```
public void setAlpha(double alpha)
```

setBeta
```
public void setBeta(double beta)
```

getBeta
```
public double getBeta()
```

getGamma
```
public double getGamma()
```

getAlpha
```
public double getAlpha()
```

showStress
```
public void showStress()
```

setOriginalPlus
```
public void setOriginalPlus(ij.ImagePlus plus)
```
Sets the backing image plus, defaulting the channel to 0 and the frame to the current frame.

Parameters:

plus -

setOriginalPlus
```
public void setOriginalPlus(ij.ImagePlus plus,
                            int channel)
```
Sets the current backing image to the provided image at the selected channel and the current frame.

Parameters:

plus -

channel -

setOriginalPlus

public void setOriginalPlus(ij.ImagePlus plus,
                            int frame,
                            int channel)

nextFrame
```
public void nextFrame()
```

setFrame
```
public void setFrame(int i)
```

previousFrame
```
public void previousFrame()
```

setNormalizerWeight

public void setNormalizerWeight(double d)

setPressure
```
public void setPressure(double p)
```

getPressure
```
public double getPressure()
```

setStericNeighborWeight

public void setStericNeighborWeight(double d)

getStericNeighborWeight

public double getStericNeighborWeight()

saveMeshes

public void saveMeshes(File f)
                throws IOException

Throws:: IOException

exportAsStl

public void exportAsStl(File f)
                 throws IOException

Throws:: IOException

exportAsWireframeStl

public void exportAsWireframeStl(File f)
                          throws IOException

Throws:: IOException

getSelectedMesh

public DeformableMesh3D getSelectedMesh(int frame)

getCurrentFrame
```
public int getCurrentFrame()
```

getSelectedTrack
```
public Track getSelectedTrack()
```

calculateVolume
```
public void calculateVolume()
```

load3DFurrows
```
public void load3DFurrows(File f)
```

saveFurrows
```
public void saveFurrows(File f)
```

notifyMeshListeners
```
public void notifyMeshListeners()
```

startEmptyTrack
```
public Track startEmptyTrack()
```
Starts a track that is not used but has a name unique to the existing tracks.

Returns:

startMeshTrack

public Track startMeshTrack(int frame,
                            DeformableMesh3D freshMesh)

calculateActinIntensity
```
public void calculateActinIntensity()
```

setCortexThickness

public void setCortexThickness(double d)

getCortexThickness
```
public double getCortexThickness()
```

calculateLineScans
```
public void calculateLineScans()
```

showCurvature
```
public void showCurvature()
```

setWeight
```
public void setWeight(double d)
```

getImageWeight
```
public double getImageWeight()
```

setDivisions
```
public void setDivisions(int i)
```

getDivisions
```
public int getDivisions()
```

generateImageEnergy

public ExternalEnergy generateImageEnergy(DeformableMesh3D mesh)

setImageEnergyType
```
public void setImageEnergyType(ImageEnergyType i)
```
The energy type will be used to decide which image energy is add during deformations.

Parameters:

i -

setRingController

public void setRingController(RingController ringController)

getRingController

public RingController getRingController()

externalEnergies
```
public void externalEnergies()
```

getExternalEnergies

public List<ExternalEnergy> getExternalEnergies(DeformableMesh3D selectedMesh)

getExternalEnergies
```
public List<ExternalEnergy> getExternalEnergies()
```
returns a list of all the external energies, except 'ring energy' affecting the currently selected mesh.

Returns:

setMeshes

public void setMeshes(List<Track> meshes)

getShortImageName
```
public String getShortImageName()
```

getNormalizeWeight
```
public double getNormalizeWeight()
```

createBinaryImage
```
public void createBinaryImage()
```

createEnergyImage
```
public void createEnergyImage()
```

createMosaicImage
```
public void createMosaicImage()
```

hasSelectedMesh
```
public boolean hasSelectedMesh()
```

selectTrackWithMesh

public void selectTrackWithMesh(DeformableMesh3D mesh)

removeMeshFromTrack

public void removeMeshFromTrack(int frame,
                                DeformableMesh3D mesh,
                                Track track)

addMeshToTrack

public void addMeshToTrack(int f,
                           DeformableMesh3D mesh,
                           Track track)

selectNextTrack
```
public void selectNextTrack()
```

selectPreviousTrack
```
public void selectPreviousTrack()
```

getAllTracks
```
public List<Track> getAllTracks()
```
Returns:

an unmodifiable list of all the mesh tracks.

addFrameListener

public void addFrameListener(FrameListener listener)

addMeshListener

public void addMeshListener(FrameListener listener)

removeMeshListener

public void removeMeshListener(FrameListener listener)

getSurfaceOffsets
```
public double[] getSurfaceOffsets()
```

getZToYScale
```
public double getZToYScale()
```

getOriginalStackDimensions

public int[] getOriginalStackDimensions()

getBounds
```
public Box3D getBounds()
```

measureAllVolumes
```
public void measureAllVolumes()
```

measureSelectedMesh
```
public void measureSelectedMesh()
```

hasNextFrame
```
public boolean hasNextFrame()
```

showFurrowValues
```
public void showFurrowValues()
```
Creates a text window with the current furrow values scaled to the image units.

exportAsPly

public void exportAsPly(File f)
                 throws IOException

Throws:: IOException

getLastSavedFile
```
public File getLastSavedFile()
```

setLastSavedFile

public void setLastSavedFile(File lastSavedFile)

isHardBoundaries
```
public boolean isHardBoundaries()
```

setHardBoundaries

public void setHardBoundaries(boolean hardBoundaries)

calculateInterfaceLineScan

public void calculateInterfaceLineScan(Track track)

calculateInterfaceLineScan

public void calculateInterfaceLineScan(int index,
                                       List<Track> tracks)

calculateInterfaceLineScans

public void calculateInterfaceLineScans()

createSubMesh

public DeformableMesh3D createSubMesh(DeformableMesh3D mesh,
                                      Set<Triangle3D> triangles)

removeMeshTrack

public void removeMeshTrack(Track track)

addMeshTrack

public void addMeshTrack(Track track)

removeFrameListener

public void removeFrameListener(FrameListener listener)

selectMeshTrack

public void selectMeshTrack(Track track)

getNChannels
```
public int getNChannels()
```

Class SegmentationModel

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

energyType

Constructor Detail

SegmentationModel

Method Detail

getDeformationCount

deformMesh

deformMeshes

deformMesh

stopRunning

setGamma

setAlpha

setBeta

getBeta

getGamma

getAlpha

showStress

setOriginalPlus

setOriginalPlus

setOriginalPlus

nextFrame

setFrame

previousFrame

setNormalizerWeight

setPressure

getPressure

setStericNeighborWeight

getStericNeighborWeight

saveMeshes

exportAsStl

exportAsWireframeStl

getSelectedMesh

getCurrentFrame

getSelectedTrack

calculateVolume

load3DFurrows

saveFurrows

notifyMeshListeners

startEmptyTrack

startMeshTrack

calculateActinIntensity

setCortexThickness

getCortexThickness

calculateLineScans

showCurvature

setWeight

getImageWeight

setDivisions

getDivisions

generateImageEnergy

setImageEnergyType

setRingController

getRingController

externalEnergies

getExternalEnergies

getExternalEnergies

setMeshes

getShortImageName

getNormalizeWeight

createBinaryImage

createEnergyImage

createMosaicImage

hasSelectedMesh

selectTrackWithMesh

removeMeshFromTrack

addMeshToTrack

selectNextTrack

selectPreviousTrack

getAllTracks

addFrameListener

addMeshListener

removeMeshListener

getSurfaceOffsets

getZToYScale

getOriginalStackDimensions