SegmentationController (Deforming Mesh 0.9.4-SNAPSHOT API)

java.lang.Object
- deformablemesh.SegmentationController

```
public class SegmentationController
extends Object
```
This manages the SegmentationModel and provides an interface for interacting with meshes through an action stack such that changes can be un-done.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static interface SegmentationController.Executable
Tasks for the exception throwing service.

Nested Classes
Modifier and Type	Class and Description
`static interface`	`SegmentationController.Executable` Tasks for the exception throwing service.

Constructor Summary

Constructors
Constructor and Description

SegmentationController(SegmentationModel model)
Creates a controller for the supplied model.

Constructors
Constructor and Description
`SegmentationController(SegmentationModel model)` Creates a controller for the supplied model.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addFrameListener(FrameListener listener)` Adds a new frame listener that gets notified whenever: nextFrame, previousFrame, setFrame, or the backing imageplus is changed.
`void`	`addMesh(DeformableMesh3D m)` Adds the mesh to the currently selected track.
`void`	`addMesh(int frame, DeformableMesh3D m)` Adds the provided mesh to the model.
`void`	`addMeshListener(FrameListener listener)` Adds a listener, that gets notified every time the displayed meshes should change.
`void`	`addTracer(Track t)` Addes a line that follows the center of mass of the provided mesh track to the current frame.
`void`	`addTransientObject(DataObject dataObject)` Adds a data object to the current meshframe, the object is "transient" and will be removed when clear transient objects is called.
`void`	`addUndoStateListener(StateListener listener)` Gets notified when the action stack updates the value.
`void`	`autotrackAvailableTracks()`
`void`	`calculateAllInterfaceTimeScans()` Iterates over all of the meshes and calculates intensity.
`void`	`calculateLineScans()` TODO remove
`void`	`calculateObscuringMeshes(double v)` Calculates the surface area over time, and the surface areas that are obscured by neighboring meshes.
`void`	`calculateSelectedInterfaceTimeScans()` Calculates the time course for the selected mesh only.
`boolean`	`canRedo()` Checks if there is an action to be undone.
`boolean`	`canUndo()` Checks if there is an action to be undone.
`void`	`centerSelectedMesh()`
`void`	`changeVolumeClipping(int minDelta, int maxDelta)` Adjust the min/max values for clipping the image.
`void`	`clearHistory()` The history can take up a lot of memory, especially for actions like deformlAllMeshes.
`void`	`clearMesh(DeformableMesh3D mesh)` Least efficient way to clear a mesh.
`void`	`clearMeshFromTrack(Track t, int f)`
`void`	`clearMeshFromTrack(Track old, int f, DeformableMesh3D mesh)` Clears the mesh specified mesh from the track at the specific time frame.
`void`	`clearSelectedMesh()` Remove the currently selected mesh, from the current frame only.
`void`	`clearTransientObjects()` clears all transient objects, objects being displayed in the 3d viewer that were added as transient objects.
`void`	`confineMesh(DeformableMesh3D mesh)` If a point is outside of the boundary, it is moved to the edge along that axis.
`DeformableMesh3D`	`copyMesh(DeformableMesh3D mesh)` Creates a copy of the provided mesh.
`void`	`createBinaryImage()` Creates an imageplus that is a binary image with pixes values 1 inside a mesh and 0 outside.
`void`	`createDataTable()`
`void`	`createEnergyImage()` Creates an image that is generated by the current image energy.
`FurrowTransformer`	`createFurrowTransform(double[] pos, double[] normal)` The provided normal and position represent a plane.
`void`	`createLabelledImage(List<Track> tracks)` Creates a labelled image of the provided tracks.
`void`	`createMosaicImage()` Creates a mosaic image, which is like a binary image, execept each mesh is labelled with it's color instead of binary.
`Image`	`createSlice(double[] pos, double[] normal)` Creates an image based on a furrow transformer built using the provided position and normal.
`Image`	`createSlice(FurrowTransformer transformer)` Creates an Image based on slicing the working volume with the plane represented by this transformer.
`void`	`curvatureSnapShot()` Takes the currently selected mesh and looks for neighbors.
`SurfacePlot`	`curvatureSurfacePlot()` Creates a 3D plot frame for the currently selected mesh, and plots the curvature on the surface.
`void`	`deformAllMeshes()` Deforms all meshes in the current frame sequentially.
`void`	`deformAllMeshes(int steps)` Deforms all meshes in the current frame for steps number of iterations, sequentially.
`void`	`deformMesh()` Deforms mesh until stopped.
`void`	`deformMesh(int count)` Deforms mesh for a set number of iterations.
`void`	`deformPartialMesh()`
`void`	`exportAsPly(File f)` Export every mesh in the current frame as a ply file with color.
`void`	`exportAsStl(File f)` Saves all of the meshes in the current frame as an ascii stl file.
`void`	`exportAsWireframeStl(File f)` Export as wire-frame mesh stl file.
`void`	`generateTrainingData(int start, int finish)` Training data consists of two images.
`List<Track>`	`getAllTracks()`
`double`	`getAlpha()`
`double`	`getBeta()`
`Box3D`	`getBounds()` Bounds of the current image being analyzed.
`int`	`getCurrentChannel()` Gets the currently selected channel.
`int`	`getCurrentFrame()` Zero based frame number.
`long`	`getCurrentState()` The action stack controls the undo/redo commands.
`int`	`getDeformationSteps()` Gets the current number of deformations that have occurred.
`int`	`getDivisions()`
`List<Exception>`	`getExecutionErrors()` For the gui to check for errors.
`double`	`getGamma()`
`double`	`getImageWeight()`
`File`	`getLastSavedFile()` For using save without save-as.
`double`	`getMaxConnectionLength()`
`DeformableMesh3D`	`getMesh()`
`MeshFrame3D`	`getMeshFrame3D()` Returns the main 3D view.
`MeshImageStack`	`getMeshImageStack()` Gets the currently selected MeshImageStack.
`boolean`	`getMeshModified()` returns true if the current state of mesh tracks has changed.
`double`	`getMinConnectionLength()`
`SegmentationModel`	`getModel()` This is being exposed to create undoable tasks it should not be used if it can be avoided.
`int`	`getNChannels()` Get the number of channels of the currently selected image.
`int`	`getNFrames()` Total number of frames in the movie.
`double`	`getNormalizeWeight()`
`int[]`	`getOriginalStackDimensions()`
`double`	`getPressure()`
`String`	`getRedoName()` Returns the name of the next action that can be redone.
`RingController`	`getRingController()` Controls the furrow.
`DeformableMesh3D`	`getSelectedMesh()`
`String`	`getSelectedMeshName()` Gets the name of the currently selected mesh.
`Track`	`getSelectedMeshTrack()`
`String`	`getShortImageName()` Returns the short image name based on the full image title with the image name extension removed.
`double`	`getStericNeighborWeight()`
`double[]`	`getSurfaceOffsets()` The origin in the 3d view is in the center of the original image.
`String`	`getUndoName()` Gets the name of the next action to be undone, if it has a name.
`Color`	`getVolumeColor()`
`double`	`getZToYScale()`
`ij.ImagePlus`	`guessMeshes(int level)` Thresholds the current image and places meshes over the individual regions.
`boolean`	`has3DViewer()` Checks for a MeshFrame3D.
`boolean`	`hasOriginalPlus()` Checks if an image is loaded.
`void`	`hideVolume()` Stops displaying the volume in the meshframe3d.
`void`	`importMeshes(File f, ImportType type)` Opens the meshfile and adds all of the meshes to the current meshes.
`void`	`initializeMesh(DeformableMesh3D mesh)` For creating a new mesh, if there is a currently selected mesh in the current frame, this starts a new mesh track.
`SurfacePlot`	`intensitySurfacePlot()` Creates an object that is used for producing an intensity plot based on the currently selected mesh and image.
`void`	`linkPossibleTrack()` If the currently selected mesh is available, this well look in the same area in the next frame and link the best possibility.
`void`	`load3DFurrows(File f)` Loads furrows, 3D plane 1 per frame.
`void`	`loadImage(String file_name)` Loads an imageplus from the provided file.
`void`	`loadMeshes(File f)` Loads meshes and replaces the current meshes.
`void`	`loadParameters(File f)` gets deformation parameters that have been saved in a file.
`void`	`lumpImports(List<Track> imports)` Groups all of the meshes into the current frame.
`void`	`maskToDistanceTransform()` Creates a distance transform with the currently selected image.
`void`	`measureAllVolumes()` Measures the volumes for all of the mesh tracks, creates a text window with the data like.
`void`	`measureSelected()` Measures the selected track through time and calculates: c_x, c_y, c_z: centroid position coordinates.
`void`	`measureVolume()` Opens a window with volume measurements for the currently selected mesh track.
`void`	`nextFrame()` Changes to the next image frame.
`void`	`plotCellCount()` Creates a plot of mesh count vs time.
`void`	`plotDisplacements()` Creates two plots.
`void`	`plotElongationsVsTime()` Finds the principle moments of Inertia and plots the anisotropy over time.
`void`	`plotTrackingStatistics()` Creates a plot with information about the frame to frame displacement of the current set of meshes.
`void`	`plotVolumeAveragedIntensityVsTime()`
`void`	`plotVolumes()` Plots the volumes of meshes over time for all of the meshes.
`void`	`previousFrame()` Moves to the previous image frame.
`void`	`recordSnapshots(int start, int end)` Creates an ImagePlus with snapshots from each frame.
`void`	`redo()` moves the action stack forward.
`void`	`relateImports(List<Track> imports)` Finds the earliest mesh frame, aligns that to the current frame
`void`	`reMesh()` Remeshes the currently selected mesh by raycasting a sphere.
`void`	`reMeshConnections(double minConnectionLength, double maxConnectionLength)` Remesh the selected mesh to the provided min and max connection lengths.
`void`	`reMeshConnections(Track track, int frame, double minConnectionLength, double maxConnectionLength)` Remeshes the current track by using the remesh connection algorithm.
`void`	`reMeshConnectionsAllMeshes(double minConnectionLength, double maxConnectionLength)` Applies the connection remesh algorith to all meshes in the current frame.
`void`	`removeFrameListener(FrameListener listener)`
`void`	`removeMeshListener(FrameListener listener)`
`void`	`removeUndoStateListener(StateListener listener)`
`void`	`renderMeshesIn2D()` Opens a new window that renders the provided meshes in 2D.
`void`	`restartMeshes()` Clears ALL of the current meshes.
`void`	`saveFurrows(File f)` Saves the furrow from each plane.
`void`	`saveMeshes(File f)` Saves the current meshes
`void`	`saveParameters(File f)` Saves the current deformation parameters to a file.
`void`	`selectChannel(int c)`
`void`	`selectImports(List<Track> imports)` Reduces the provided meshes to only meshes in the currently selected frame.
`void`	`selectMesh(DeformableMesh3D mesh)` Attempts to select the track that contains the provided mesh.
`void`	`selectMeshTrack(Track track)` Overload for convenience.
`void`	`selectNextMeshTrack()` Changes the currently selected track to be the next one.
`void`	`selectNone()` Causes no mesh track to be selected.
`void`	`selectPreviousMeshTrack()` Changes to the previously selected track.
`void`	`setAlpha(double d)` Deformation parameter, effectively the spring-like stiffness connections.
`void`	`setBeta(double d)` deformation parameter: represents the bending stiffness.
`void`	`setDivisions(int d)` When a new mesh is created, it is subdivided this number of times.
`void`	`setFurrowForCurrentFrame(double[] center, double[] normal)` Sets the position and normal of the furrow.
`void`	`setGamma(double gamma)` Deformation parameter, high values limit the rate of deformation.
`void`	`setHardBoundaries(boolean v)` Hard boundaries cause a mesh to be confined after each step during deformation.
`void`	`setImageEnergyType(ImageEnergyType selectedItem)` The type of image energy that will be used.
`void`	`setMaxConnectionLength(double mcl)` Set the maximum connection length that is used when doing a connection remesh.
`void`	`setMesh(Track track, int frame, DeformableMesh3D mesh)` Sets the provided mesh to be the mesh for the provided track at the specified frame.
`void`	`setMeshes(List<Track> tracks, int frame, List<DeformableMesh3D> meshes)` Adds all of the provided meshes to the corresponding track.
`void`	`setMeshFrame3D(MeshFrame3D meshFrame3D)` Sets up the provided meshframe3d as the main threed display.
`void`	`setMeshTracks(List<Track> replacements)` Replaces the current tracks with the provided.
`void`	`setMinConnectionLength(double mcl)` Gets the minimum connection length when doing a connection remesh.
`void`	`setNormalizerWeight(double d)` Turns on an external energy that tries to normalize triangle sizes.
`void`	`setOriginalPlus(ij.ImagePlus plus)` Sets the current image, and sets it on channel 0.
`void`	`setOriginalPlus(ij.ImagePlus plus, int channel)` Causes the provided image to be the main backing image data.
`void`	`setPressure(double d)` For shrinking or growing a mesh.
`void`	`setRigidBoundaries(boolean selected)` When true, deforming meshes are confined at each step.
`void`	`setStericNeighborWeight(double d)` Causes a 'steric' force from neighboring meshes to prevent mesh overlap.
`void`	`setVolumeColor(Color color)` The color the image volume is display as, when the image volume is showing.
`void`	`setWeight(double d)` Sets the magnitude of force the image causes on the mesh.
`void`	`showBinaryBlob()` Shows the volume of the currently selected mesh by adding a voxel transient object, similar to the way show volume works, but the result is binary and colored.
`void`	`showCurvature()` TODO remove
`void`	`showForces()` Shows forces on the currently selected mesh.
`void`	`showForces(DeformableMesh3D mesh)` Creates a set of vectors to show how the mesh will deform based on the image energy and external forces.
`void`	`showFurrowValues()` Creates a text window with the current furrow values, position in image units and normal.
`double[]`	`showInertialVector()` Shows a two vectors.
`void`	`showStress()` TODO remove
`void`	`showTexturedMeshSurface()` Adds a transient data object using a 3D volume texture and a surface with the currently selected mesh geometry.
`void`	`showVolume()` Shows the volume data in the meshframe.
`void`	`showVolumeClippingDialog()`
`void`	`splitMesh()`
`void`	`splitMeshTrack()` Splits this track into two with all meshes from, and up to the current frame in one track and all of the subsequent meshes in a new track.
`void`	`startNewMeshTrack(int frame, DeformableMesh3D mesh)` Starts a new mesh track with one mesh on the specified frame.
`void`	`startNewMeshTracks(List<DeformableMesh3D> meshes)` Starts a new Track for each of provided meshes.
`void`	`stopRunning()` Primarily used to stop deforming a mesh.
`void`	`submit(SegmentationController.Executable runnable)` Method for submitting jobs to the models main loops.
`void`	`takeSnapShot()` Creates a snapshot of the current 3d view and creates an image plus window.
`void`	`toFrame(int f)` Sets the frame.
`void`	`toggleSurface()` Toggles displaying the surface of the currently selected mesh track.
`void`	`trackMesh()` Creates a copy of the current mesh, advances a frame and adds it to the current track.
`void`	`trackMesh(Track track, int frame)` Extands the track to (frame + 1) provided by copying the deformable mesh at frame.
`void`	`trackMeshBackwards()` Copies the current mesh, moves to the previous frame and adds the copy to the currently selected track.
`void`	`undo()` Moves the action stack back.
`void`	`validateMeshes()`

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

- Constructor Detail
  - SegmentationController
```
public SegmentationController(SegmentationModel model)
```
    Creates a controller for the supplied model.
    
    Parameters:
    
    model - data that will be controlled.
- Method Detail
  - setGamma
```
public void setGamma(double gamma)
```
    Deformation parameter, high values limit the rate of deformation.
    
    Parameters:
    
    gamma - a number greater than 0.
  - setAlpha
```
public void setAlpha(double d)
```
    Deformation parameter, effectively the spring-like stiffness connections.
    
    Parameters:
    
    d - a number greater than 0
  - setPressure
```
public void setPressure(double d)
```
    For shrinking or growing a mesh.
    
    Parameters:
    
    d - Non-zero values create an effective force that either causes the mesh to expand (positive) or shrink (negative).
  - setStericNeighborWeight
```
public void setStericNeighborWeight(double d)
```
    Causes a 'steric' force from neighboring meshes to prevent mesh overlap.
    
    Parameters:
    
    d - magnitude of repulsion. 0 turns off effect.
  - setWeight
```
public void setWeight(double d)
```
    Sets the magnitude of force the image causes on the mesh.
    
    Parameters:
    
    d - can be positive or negative.
  - setDivisions
```
public void setDivisions(int d)
```
    When a new mesh is created, it is subdivided this number of times. 0 deformations corresponds to 20 triangles. Each division divides the triangles into 4, so there will be 20*4**N triangles. 5 divisions is 20480 triangles, which displays fine, but not practical for deforming.
    
    Parameters:
    
    d - number of times mesh is subdivided.
  - getGamma
```
public double getGamma()
```
  - getAlpha
```
public double getAlpha()
```
  - getPressure
```
public double getPressure()
```
  - getMinConnectionLength
```
public double getMinConnectionLength()
```
  - setMinConnectionLength
```
public void setMinConnectionLength(double mcl)
```
    Gets the minimum connection length when doing a connection remesh. Connections shorter that this will be replaced if possible.
    
    Parameters:
    
    mcl - must be greater than 0 less than max.
  - getMaxConnectionLength
```
public double getMaxConnectionLength()
```
  - setMaxConnectionLength
```
public void setMaxConnectionLength(double mcl)
```
    Set the maximum connection length that is used when doing a connection remesh. Connections longer than this length will be split. Should probably be more than to about double the minimum length.
    
    Parameters:
    
    mcl - greater than zero, greater than minimum length.
  - addMeshListener
```
public void addMeshListener(FrameListener listener)
```
    Adds a listener, that gets notified every time the displayed meshes should change. For example during track changes where a mesh is added or removed; When mesh tracks are set; When the selected track is changed; When clearTransientObjects is called.
    
    Parameters:
    
    listener - cannot be null.
  - removeMeshListener
```
public void removeMeshListener(FrameListener listener)
```
  - getImageWeight
```
public double getImageWeight()
```
  - getDivisions
```
public int getDivisions()
```
  - clearMesh
```
public void clearMesh(DeformableMesh3D mesh)
```
    Least efficient way to clear a mesh. Attempts to locate the provided mesh in within a track and remove it.
    
    Parameters:
    
    mesh - mesh that will be removed from a track.
    
    See Also:
    
    clearMeshFromTrack(Track, int, DeformableMesh3D)
  - clearMeshFromTrack
```
public void clearMeshFromTrack(Track t,
                               int f)
```
    Parameters:
    
    t - track that will lose a mesh
    
    f - frame the mesh will be removed from if a mesh exists.
    
    See Also:
    
    clearMeshFromTrack(Track, int, DeformableMesh3D)
  - clearMeshFromTrack
```
public void clearMeshFromTrack(Track old,
                               int f,
                               DeformableMesh3D mesh)
```
    Clears the mesh specified mesh from the track at the specific time frame.
    
    Parameters:
    
    old - track that mesh will be removed from.
    
    f - time frame.
    
    mesh - mesh to be removed.
  - clearSelectedMesh
```
public void clearSelectedMesh()
```
    Remove the currently selected mesh, from the current frame only.
  - addUndoStateListener
```
public void addUndoStateListener(StateListener listener)
```
    Gets notified when the action stack updates the value.
    
    Parameters:
    
    listener -
  - removeUndoStateListener
```
public void removeUndoStateListener(StateListener listener)
```
  - undo
```
public void undo()
```
    Moves the action stack back.
  - redo
```
public void redo()
```
    moves the action stack forward.
  - canUndo
```
public boolean canUndo()
```
    Checks if there is an action to be undone. Primarily used for the menu.
    
    Returns:
  - canRedo
```
public boolean canRedo()
```
    Checks if there is an action to be undone. Primarily used for the menu.
    
    Returns:
  - submit
```
public void submit(SegmentationController.Executable runnable)
```
    Method for submitting jobs to the models main loops. Especially for jobs that should be performed after the current jobs have finished. For example when stop has been clicked and deforming is indicated to stop, but it has not completed yet. This can be used from javascript console by declaring a function. eg. controller.submit(function(){ print("Made it through the queue");}); Would not print until everything submitted before has finished.
    
    Parameters:
    
    runnable -
  - previousFrame
```
public void previousFrame()
```
    Moves to the previous image frame.
  - nextFrame
```
public void nextFrame()
```
    Changes to the next image frame.
  - toFrame
```
public void toFrame(int f)
```
    Sets the frame.
    
    Parameters:
    
    f - desired frame, silently fails if out of range.
  - takeSnapShot
```
public void takeSnapShot()
```
    Creates a snapshot of the current 3d view and creates an image plus window. If this does not work It is possible to reset the offscreen canvas used for taking snapshots using This is also available by pressing 's' when the 3D canvas window is selected.
    
    See Also:
    
    MeshFrame3D
  - recordSnapshots
```
public void recordSnapshots(int start,
                            int end)
```
    Creates an ImagePlus with snapshots from each frame. This is also available as a menu item.
    
    Parameters:
    
    start - the first frame to be imaged, frame 1 is 0.
    
    end - last frame, inclusive.
  - centerSelectedMesh
```
public void centerSelectedMesh()
```
  - reMesh
```
public void reMesh()
```
    Remeshes the currently selected mesh by raycasting a sphere. The number of triangles is determined by the divisions parameter.
  - maskToDistanceTransform
```
public void maskToDistanceTransform()
```
    Creates a distance transform with the currently selected image. It is expected that the image is a mask, 0 or non-zero values.
  - getMeshImageStack
```
public MeshImageStack getMeshImageStack()
```
    Gets the currently selected MeshImageStack.
    
    Returns:
  - reMeshConnections
```
public void reMeshConnections(Track track,
                              int frame,
                              double minConnectionLength,
                              double maxConnectionLength)
```
    Remeshes the current track by using the remesh connection algorithm.
    
    Parameters:
    
    track - track to be remeshed.
    
    frame - the frame # of the mesh to be remeshed.
    
    minConnectionLength - connections shorter that the minimum length will be removed.
    
    maxConnectionLength - connections long than the maximum length will be split in two.
  - setMeshes
```
public void setMeshes(List<Track> tracks,
                      int frame,
                      List<DeformableMesh3D> meshes)
```
    Adds all of the provided meshes to the corresponding track. The tracks and meshes are associated by order.
    
    Parameters:
    
    tracks -
    
    frame -
    
    meshes -
  - setMesh
```
public void setMesh(Track track,
                    int frame,
                    DeformableMesh3D mesh)
```
    Sets the provided mesh to be the mesh for the provided track at the specified frame. This will replace any existing meshes in the provided frame.
    
    Parameters:
    
    track - track that will acquire the new mesh.
    
    frame - frame the mesh will be placed at.
    
    mesh - the mesh that will be part of the track.
  - generateTrainingData
```
public void generateTrainingData(int start,
                                 int finish)
```
    Training data consists of two images. The original image, and a labelled image which is an a bit image. The first bit represents the mesh, the second bit represents inside, or outside of the mesh and the last 6 bits are the distance transform. This will populate two folders, images and labels, with the respective z-stacks for each time point.
    
    Parameters:
    
    start - 0 based time frame. First frame inclusive.
    
    finish - 0 based time frame. Last frame inclusive.
  - reMeshConnections
```
public void reMeshConnections(double minConnectionLength,
                              double maxConnectionLength)
```
    Remesh the selected mesh to the provided min and max connection lengths.
    
    Parameters:
    
    minConnectionLength - normalized length
    
    maxConnectionLength - normalized length
    
    See Also:
    
    reMeshConnections(Track, int, double, double)
  - getNChannels
```
public int getNChannels()
```
    Get the number of channels of the currently selected image.
    
    Returns:
  - getCurrentChannel
```
public int getCurrentChannel()
```
    Gets the currently selected channel.
    
    Returns:
  - plotCellCount
```
public void plotCellCount()
```
    Creates a plot of mesh count vs time.
  - plotTrackingStatistics
```
public void plotTrackingStatistics()
```
    Creates a plot with information about the frame to frame displacement of the current set of meshes.
  - plotVolumes
```
public void plotVolumes()
```
    Plots the volumes of meshes over time for all of the meshes. Each track is a continuous set of data points.
  - plotDisplacements
```
public void plotDisplacements()
```
    Creates two plots. Displacements vs Time per tracks and a histogram of displacements.
  - plotElongationsVsTime
```
public void plotElongationsVsTime()
```
    Finds the principle moments of Inertia and plots the anisotropy over time.
  - showInertialVector
```
public double[] showInertialVector()
```
    Shows a two vectors. One indicating the moment of inertia of the collective mesh rotation. One indicates the angular momentum of an equivalent rigid body rotation.
    
    Returns:
    
    {px, py, pz}
  - selectNone
```
public void selectNone()
```
    Causes no mesh track to be selected.
  - clearHistory
```
public void clearHistory()
```
    The history can take up a lot of memory, especially for actions like deformlAllMeshes.
  - guessMeshes
```
public ij.ImagePlus guessMeshes(int level)
```
    Thresholds the current image and places meshes over the individual regions. Checks for overlap with existing meshes and doesn't place meshes if there is too much overlap.
    
    Parameters:
    
    level - The value used for thresholding the image. Expected to work on integer images.
    
    Returns:
    
    an ImagePlus with the thresholded image.
  - reMeshConnectionsAllMeshes
```
public void reMeshConnectionsAllMeshes(double minConnectionLength,
                                       double maxConnectionLength)
```
    Applies the connection remesh algorith to all meshes in the current frame.
    
    Parameters:
    
    minConnectionLength - normalized length for min connection lengths.
    
    maxConnectionLength - normalized length for max connection lengths.
    
    See Also:
    
    reMeshConnections(Track, int, double, double)
  - curvatureSnapShot
```
public void curvatureSnapShot()
```
    Takes the currently selected mesh and looks for neighbors. Locates 'touching' faces and a dds transient objects that show the touching surface. Also produces curvature histograms, for the whole cell, and the regions touch.
  - curvatureSurfacePlot
```
public SurfacePlot curvatureSurfacePlot()
```
    Creates a 3D plot frame for the currently selected mesh, and plots the curvature on the surface.
    
    Returns:
    
    an object for generating a surface plot.
  - intensitySurfacePlot
```
public SurfacePlot intensitySurfacePlot()
```
    Creates an object that is used for producing an intensity plot based on the currently selected mesh and image.
    
    Returns:
  - showBinaryBlob
```
public void showBinaryBlob()
```
    Shows the volume of the currently selected mesh by adding a voxel transient object, similar to the way show volume works, but the result is binary and colored.
  - restartMeshes
```
public void restartMeshes()
```
    Clears ALL of the current meshes.
  - getLastSavedFile
```
public File getLastSavedFile()
```
    For using save without save-as.
    
    Returns:
  - addMesh
```
public void addMesh(DeformableMesh3D m)
```
    Adds the mesh to the currently selected track.
    
    Parameters:
    
    m -
    
    See Also:
    
    addMesh(int frame, DeformableMesh3D mesh)
  - startNewMeshTrack
```
public void startNewMeshTrack(int frame,
                              DeformableMesh3D mesh)
```
    Starts a new mesh track with one mesh on the specified frame.
    
    Parameters:
    
    frame - frame mesh is added to. Note 0 based indexing.
    
    mesh -
  - selectNextMeshTrack
```
public void selectNextMeshTrack()
```
    Changes the currently selected track to be the next one.
  - selectPreviousMeshTrack
```
public void selectPreviousMeshTrack()
```
    Changes to the previously selected track.
  - selectMeshTrack
```
public void selectMeshTrack(Track track)
```
    Overload for convenience.
    
    Parameters:
    
    track - track that will be selected. can be null
  - selectMesh
```
public void selectMesh(DeformableMesh3D mesh)
```
    Attempts to select the track that contains the provided mesh.
    
    Parameters:
    
    mesh -
  - addMesh
```
public void addMesh(int frame,
                    DeformableMesh3D m)
```
    Adds the provided mesh to the model. The behavior is conditional on the currently selected track. If there is a selected track, the mesh is added to the selected track. Replacing any previous meshes at the at the provided frame. If there isn't a selected track, then a new track is started.
    
    Parameters:
    
    frame -
    
    m -
  - addTracer
```
public void addTracer(Track t)
```
    Addes a line that follows the center of mass of the provided mesh track to the current frame.
    
    Parameters:
    
    t -
  - startNewMeshTracks
```
public void startNewMeshTracks(List<DeformableMesh3D> meshes)
```
    Starts a new Track for each of provided meshes. Used with guess meshes.
    
    Parameters:
    
    meshes - If the list is empty, this is a non-op.
  - createFurrowTransform
```
public FurrowTransformer createFurrowTransform(double[] pos,
                                               double[] normal)
```
    The provided normal and position represent a plane. This transformer is used for transforming between the plane coordinates, and world coordinates.
    
    Parameters:
    
    pos - center of the plane
    
    normal - normal of the plane.
    
    Returns:
    
    for transforming coordinates.
  - createSlice
```
public Image createSlice(double[] pos,
                         double[] normal)
```
    Creates an image based on a furrow transformer built using the provided position and normal. Primarily used for GUI.
    
    Parameters:
    
    pos - center of plane
    
    normal - direction of normal
    
    Returns:
    
    sliced image.
  - createSlice
```
public Image createSlice(FurrowTransformer transformer)
```
    Creates an Image based on slicing the working volume with the plane represented by this transformer. Primarily used for GUI.
    
    Parameters:
    
    transformer -
    
    Returns:
  - addTransientObject
```
public void addTransientObject(DataObject dataObject)
```
    Adds a data object to the current meshframe, the object is "transient" and will be removed when clear transient objects is called.
    
    Parameters:
    
    dataObject - 3d display object
  - clearTransientObjects
```
public void clearTransientObjects()
```
    clears all transient objects, objects being displayed in the 3d viewer that were added as transient objects.
  - measureVolume
```
public void measureVolume()
```
    Opens a window with volume measurements for the currently selected mesh track. If There is a furrow, then the volume is split into front and back halfs.
  - calculateAllInterfaceTimeScans
```
public void calculateAllInterfaceTimeScans()
```
    Iterates over all of the meshes and calculates intensity. (a bit intense.)
  - calculateSelectedInterfaceTimeScans
```
public void calculateSelectedInterfaceTimeScans()
```
    Calculates the time course for the selected mesh only.
  - calculateLineScans
```
public void calculateLineScans()
```
    TODO remove
    
    See Also:
    
    MeshAnalysis
  - showStress
```
public void showStress()
```
    TODO remove
  - showCurvature
```
public void showCurvature()
```
    TODO remove
  - showVolume
```
public void showVolume()
```
    Shows the volume data in the meshframe. The program is much slower with the volume showing. It can be faster to adjust min/max (contrast) and set the frame with the volume hidden.
  - setImageEnergyType
```
public void setImageEnergyType(ImageEnergyType selectedItem)
```
    The type of image energy that will be used.
    
    Parameters:
    
    selectedItem - enum to select which image energy will be created.
  - hideVolume
```
public void hideVolume()
```
    Stops displaying the volume in the meshframe3d.
  - changeVolumeClipping
```
public void changeVolumeClipping(int minDelta,
                                 int maxDelta)
```
    Adjust the min/max values for clipping the image. Any values less than minDelta are transparent, and values above maxDelta are opaque.
    
    Parameters:
    
    minDelta -
    
    maxDelta -
  - showVolumeClippingDialog
```
public void showVolumeClippingDialog()
```
  - deformMesh
```
public void deformMesh()
```
    Deforms mesh until stopped.
  - splitMeshTrack
```
public void splitMeshTrack()
```
    Splits this track into two with all meshes from, and up to the current frame in one track and all of the subsequent meshes in a new track.
  - validateMeshes
```
public void validateMeshes()
```
  - splitMesh
```
public void splitMesh()
```
  - deformPartialMesh
```
public void deformPartialMesh()
```
  - showTexturedMeshSurface
```
public void showTexturedMeshSurface()
```
    Adds a transient data object using a 3D volume texture and a surface with the currently selected mesh geometry.
  - deformAllMeshes
```
public void deformAllMeshes()
```
    Deforms all meshes in the current frame sequentially.
  - deformAllMeshes
```
public void deformAllMeshes(int steps)
```
    Deforms all meshes in the current frame for steps number of iterations, sequentially. If steps is < 0 then it will deform for Integer.MAX_VALUE iterations...which will probably take forever.
    
    Parameters:
    
    steps -
  - confineMesh
```
public void confineMesh(DeformableMesh3D mesh)
```
    If a point is outside of the boundary, it is moved to the edge along that axis.
    
    Parameters:
    
    mesh -
  - setHardBoundaries
```
public void setHardBoundaries(boolean v)
```
    Hard boundaries cause a mesh to be confined after each step during deformation.
    
    Parameters:
    
    v -
    
    See Also:
    
    confineMesh(DeformableMesh3D)
  - deformMesh
```
public void deformMesh(int count)
```
    Deforms mesh for a set number of iterations.
    
    Parameters:
    
    count - number of iterations, if less than zero, it continues to deform until stopped.
  - copyMesh
```
public DeformableMesh3D copyMesh(DeformableMesh3D mesh)
```
    Creates a copy of the provided mesh.
    
    Parameters:
    
    mesh -
    
    Returns:
  - trackMesh
```
public void trackMesh(Track track,
                      int frame)
```
    Extands the track to (frame + 1) provided by copying the deformable mesh at frame.
    
    Parameters:
    
    track - track to be extended.
    
    frame - initial frame
  - trackMesh
```
public void trackMesh()
```
    Creates a copy of the current mesh, advances a frame and adds it to the current track.
  - trackMeshBackwards
```
public void trackMeshBackwards()
```
    Copies the current mesh, moves to the previous frame and adds the copy to the currently selected track.
  - stopRunning
```
public void stopRunning()
```
    Primarily used to stop deforming a mesh.
  - setOriginalPlus
```
public void setOriginalPlus(ij.ImagePlus plus)
```
    Sets the current image, and sets it on channel 0. Attempts to stay on the same frame.
    
    Parameters:
    
    plus - new backing image.
  - setOriginalPlus
```
public void setOriginalPlus(ij.ImagePlus plus,
                            int channel)
```
    Causes the provided image to be the main backing image data. Tries to stay on the current frame if possible.
    
    Parameters:
    
    plus -
  - selectChannel
```
public void selectChannel(int c)
```
  - saveMeshes
```
public void saveMeshes(File f)
```
    Saves the current meshes
    
    Parameters:
    
    f - where they'll be saved.
  - getCurrentState
```
public long getCurrentState()
```
    The action stack controls the undo/redo commands. Each time a new command is posted and performed it updates the id. This returns the current id of the action stack.
    
    Returns:
    
    id of current state, incremented by one each time a new action is posed.
  - loadMeshes
```
public void loadMeshes(File f)
```
    Loads meshes and replaces the current meshes.
    
    Parameters:
    
    f -
  - importMeshes
```
public void importMeshes(File f,
                         ImportType type)
```
    Opens the meshfile and adds all of the meshes to the current meshes. They type determines how meshes are added. aligned: the frame of the imported meshes does not change. relative: The first frame of the meshes being imported are set to be the current frame. This can be good for working with selected frames of a movie. Eg. Segment by hand, frames 5-10, then move to frame 5 and import relative. lumped: All of the meshes in the importing file are imported into the current frame. select: Only meshes from the current frame of the selected meshfile are imported to the current frame.
    
    Parameters:
    
    f -
    
    type -
  - lumpImports
```
public void lumpImports(List<Track> imports)
```
    Groups all of the meshes into the current frame. New tracks are created for tracks with multiple meshes.
    
    Parameters:
    
    imports -
  - relateImports
```
public void relateImports(List<Track> imports)
```
    Finds the earliest mesh frame, aligns that to the current frame
    
    Parameters:
    
    imports -
  - selectImports
```
public void selectImports(List<Track> imports)
```
    Reduces the provided meshes to only meshes in the currently selected frame.
    
    Parameters:
    
    imports - list of tracks that will be modified to only have tracks with meshes in the current frame.
  - renderMeshesIn2D
```
public void renderMeshesIn2D()
```
    Opens a new window that renders the provided meshes in 2D.
  - setMeshTracks
```
public void setMeshTracks(List<Track> replacements)
```
    Replaces the current tracks with the provided. Used for the mesh track manager.
    
    Parameters:
    
    replacements -
  - exportAsStl
```
public void exportAsStl(File f)
```
    Saves all of the meshes in the current frame as an ascii stl file.
    
    Parameters:
    
    f -
  - exportAsWireframeStl
```
public void exportAsWireframeStl(File f)
```
    Export as wire-frame mesh stl file.
    
    Parameters:
    
    f -
  - load3DFurrows
```
public void load3DFurrows(File f)
```
    Loads furrows, 3D plane 1 per frame.
    
    Parameters:
    
    f -
  - saveFurrows
```
public void saveFurrows(File f)
```
    Saves the furrow from each plane.
    
    Parameters:
    
    f -
  - getExecutionErrors
```
public List<Exception> getExecutionErrors()
```
    For the gui to check for errors.
    
    Returns:
  - getCurrentFrame
```
public int getCurrentFrame()
```
    Zero based frame number. The displayed frame number is 1 based.
    
    Returns:
  - loadImage
```
public void loadImage(String file_name)
```
    Loads an imageplus from the provided file.
    
    Parameters:
    
    file_name -
  - getMesh
```
public DeformableMesh3D getMesh()
```
    Returns:
    
    currently selected mesh.
  - getSelectedMeshTrack
```
public Track getSelectedMeshTrack()
```
    Returns:
    
    currently selected mesh track.
  - getShortImageName
```
public String getShortImageName()
```
    Returns the short image name based on the full image title with the image name extension removed.
    
    Returns:
  - setBeta
```
public void setBeta(double d)
```
    deformation parameter: represents the bending stiffness.
    
    Parameters:
    
    d -
  - getBeta
```
public double getBeta()
```
  - setNormalizerWeight
```
public void setNormalizerWeight(double d)
```
    Turns on an external energy that tries to normalize triangle sizes.
    
    Parameters:
    
    d -
  - getNormalizeWeight
```
public double getNormalizeWeight()
```
  - createBinaryImage
```
public void createBinaryImage()
```
    Creates an imageplus that is a binary image with pixes values 1 inside a mesh and 0 outside.
    
    See Also:
    
    DeformableMesh3DTools.createBinaryRepresentation(MeshImageStack, DeformableMesh3D)
  - createLabelledImage
```
public void createLabelledImage(List<Track> tracks)
```
    Creates a labelled image of the provided tracks. The labels are not related frame to frame.
  - initializeMesh
```
public void initializeMesh(DeformableMesh3D mesh)
```
    For creating a new mesh, if there is a currently selected mesh in the current frame, this starts a new mesh track. If there isn't then addMesh is used.
    
    Parameters:
    
    mesh -
    
    See Also:
    
    addMesh(int, DeformableMesh3D)
  - getAllTracks
```
public List<Track> getAllTracks()
```
    Returns:
    
    an unmodifiable view of the current mesh tracks.
  - getSelectedMesh
```
public DeformableMesh3D getSelectedMesh()
```
    Returns:
    
    The mesh from the currently selected mesh track in the current frame. Can be null.
  - getVolumeColor
```
public Color getVolumeColor()
```
    Returns:
    
    Color that is used to display the current image as a volume in the 3D canvas.
  - setVolumeColor
```
public void setVolumeColor(Color color)
```
    The color the image volume is display as, when the image volume is showing.
    
    Parameters:
    
    color -
  - getZToYScale
```
public double getZToYScale()
```
    Returns:
    
    the ration of distance between slices to the height of a pixel.
  - getOriginalStackDimensions
```
public int[] getOriginalStackDimensions()
```
    Returns:
    
    {width (pixels), height(pixels), slices}
  - getSurfaceOffsets
```
public double[] getSurfaceOffsets()
```
    The origin in the 3d view is in the center of the original image.
    
    Returns:
  - getRingController
```
public RingController getRingController()
```
    Controls the furrow.
    
    Returns:
  - getBounds
```
public Box3D getBounds()
```
    Bounds of the current image being analyzed.
    
    Returns:
  - createMosaicImage
```
public void createMosaicImage()
```
    Creates a mosaic image, which is like a binary image, execept each mesh is labelled with it's color instead of binary.
  - measureAllVolumes
```
public void measureAllVolumes()
```
    Measures the volumes for all of the mesh tracks, creates a text window with the data like. #frame\ttrack1\ttrack2 ... If a track doesn't exist in a particular frame, then it's volume is -1.
  - hasOriginalPlus
```
public boolean hasOriginalPlus()
```
    Checks if an image is loaded.
    
    Returns:
  - getNFrames
```
public int getNFrames()
```
    Total number of frames in the movie.
    
    Returns:
  - toggleSurface
```
public void toggleSurface()
```
    Toggles displaying the surface of the currently selected mesh track.
  - createDataTable
```
public void createDataTable()
```
  - plotVolumeAveragedIntensityVsTime
```
public void plotVolumeAveragedIntensityVsTime()
```
  - measureSelected
```
public void measureSelected()
```
    Measures the selected track through time and calculates: c_x, c_y, c_z: centroid position coordinates. dmean: mean distance of nodes to centroid. dmax: max distance of nodes to centroid. dmin: min distance of nodes to centroid. Eigen values and vectors lambda1, lambda2, lambda3: eigen values. v1_x, v1_y, v1_z: first eigen vector. v2_x, v2_y, v2_z: second eigen vector. v3_x, v3_y, v3_z: third eigen vector.
  - showFurrowValues
```
public void showFurrowValues()
```
    Creates a text window with the current furrow values, position in image units and normal.
  - exportAsPly
```
public void exportAsPly(File f)
```
    Export every mesh in the current frame as a ply file with color.
    
    Parameters:
    
    f -
  - getSelectedMeshName
```
public String getSelectedMeshName()
```
    Gets the name of the currently selected mesh.
    
    Returns:
  - calculateObscuringMeshes
```
public void calculateObscuringMeshes(double v)
```
    Calculates the surface area over time, and the surface areas that are obscured by neighboring meshes.
    
    Parameters:
    
    v - cutoff distance from the center of the triangle along the normal to another triangle. Units are the units of the image.
  - getMeshModified
```
public boolean getMeshModified()
```
    returns true if the current state of mesh tracks has changed.
    
    Returns:
  - getDeformationSteps
```
public int getDeformationSteps()
```
    Gets the current number of deformations that have occurred.
    
    Returns:
  - saveParameters
```
public void saveParameters(File f)
```
    Saves the current deformation parameters to a file.
    
    Parameters:
    
    f -
  - loadParameters
```
public void loadParameters(File f)
```
    gets deformation parameters that have been saved in a file.
    
    Parameters:
    
    f -
    
    See Also:
    
    PropertySaver
  - setRigidBoundaries
```
public void setRigidBoundaries(boolean selected)
```
    When true, deforming meshes are confined at each step.
    
    Parameters:
    
    selected -
  - getUndoName
```
public String getUndoName()
```
    Gets the name of the next action to be undone, if it has a name.
    
    Returns:
    
    ActionStack#getUndoableActionName
  - getRedoName
```
public String getRedoName()
```
    Returns the name of the next action that can be redone.
    
    Returns:
    
    ActionStack#getRedoableActionName()
  - getStericNeighborWeight
```
public double getStericNeighborWeight()
```
  - showForces
```
public void showForces()
```
    Shows forces on the currently selected mesh. First clears any external energies\ then shows any updates.
  - createEnergyImage
```
public void createEnergyImage()
```
    Creates an image that is generated by the current image energy.
  - showForces
```
public void showForces(DeformableMesh3D mesh)
```
    Creates a set of vectors to show how the mesh will deform based on the image energy and external forces. The vectors are added as transient objects.
    
    Parameters:
    
    mesh -
  - has3DViewer
```
public boolean has3DViewer()
```
    Checks for a MeshFrame3D.
    
    Returns:
  - getModel
```
public SegmentationModel getModel()
```
    This is being exposed to create undoable tasks it should not be used if it can be avoided.
    
    Returns:
  - setFurrowForCurrentFrame
```
public void setFurrowForCurrentFrame(double[] center,
                                     double[] normal)
```
    Sets the position and normal of the furrow.
    
    Parameters:
    
    center -
    
    normal -
    
    See Also:
    
    RingController
  - setMeshFrame3D
```
public void setMeshFrame3D(MeshFrame3D meshFrame3D)
```
    Sets up the provided meshframe3d as the main threed display.
    
    Parameters:
    
    meshFrame3D -
  - getMeshFrame3D
```
public MeshFrame3D getMeshFrame3D()
```
    Returns the main 3D view. This can be used to set the background color.
    
    Returns:
  - addFrameListener
```
public void addFrameListener(FrameListener listener)
```
    Adds a new frame listener that gets notified whenever: nextFrame, previousFrame, setFrame, or the backing imageplus is changed.
    
    Parameters:
    
    listener -
  - linkPossibleTrack
```
public void linkPossibleTrack()
```
    If the currently selected mesh is available, this well look in the same area in the next frame and link the best possibility.
  - removeFrameListener
```
public void removeFrameListener(FrameListener listener)
```
  - autotrackAvailableTracks
```
public void autotrackAvailableTracks()
```

Class SegmentationController

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SegmentationController

Method Detail

setGamma

setAlpha

setPressure

setStericNeighborWeight

setWeight

setDivisions

getGamma

getAlpha

getPressure

getMinConnectionLength

setMinConnectionLength

getMaxConnectionLength

setMaxConnectionLength

addMeshListener

removeMeshListener

getImageWeight

getDivisions

clearMesh

clearMeshFromTrack

clearMeshFromTrack

clearSelectedMesh

addUndoStateListener

removeUndoStateListener

undo

redo

canUndo

canRedo

submit

previousFrame

nextFrame

toFrame

takeSnapShot

recordSnapshots

centerSelectedMesh

reMesh

maskToDistanceTransform

getMeshImageStack

reMeshConnections

setMeshes

setMesh

generateTrainingData

reMeshConnections

getNChannels

getCurrentChannel

plotCellCount

plotTrackingStatistics

plotVolumes

plotDisplacements

plotElongationsVsTime

showInertialVector

selectNone

clearHistory

guessMeshes

reMeshConnectionsAllMeshes

curvatureSnapShot

curvatureSurfacePlot

intensitySurfacePlot

showBinaryBlob

restartMeshes

getLastSavedFile

addMesh

startNewMeshTrack

selectNextMeshTrack

selectPreviousMeshTrack

selectMeshTrack

selectMesh

addMesh

addTracer

startNewMeshTracks

createFurrowTransform

createSlice

createSlice