DeformableMesh3D (Deforming Mesh 0.9.4-SNAPSHOT API)

java.lang.Object
- deformablemesh.geometry.DeformableMesh3D

Direct Known Subclasses:

NewtonMesh3D
```
public class DeformableMesh3D
extends Object
```
3D mesh that will be used for segmenting cells in 3D. A collection of Nodes, triangles and connections that represent a mesh in 3D User: msmith Date: 7/2/13 Time: 7:57 AM To change this template use File | Settings | File Templates.

Field Summary

Fields
Modifier and Type	Field and Description
`double`	`ALPHA`
`double`	`BETA`
`int[]`	`connection_index`
`List<Connection3D>`	`connections`
`DeformableMeshDataObject`	`data_object`
`double`	`GAMMA`
`List<Node3D>`	`nodes`
`static double[]`	`ORIGIN`
`double[]`	`positions`
`int[]`	`triangle_index`
`List<Triangle3D>`	`triangles`

Constructor Summary

Constructors
Constructor and Description
`DeformableMesh3D(double[] positions, int[] connection_indices, int[] triangle_indices)`
`DeformableMesh3D(List<double[]> node_positions, List<int[]> connection_indices, List<int[]> triangle_indices)` Creates a deformable mesh in 3d.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addExternalEnergy(ExternalEnergy energy)`
`List<double[]>`	`calculateCurvature()`
`ArrayList<double[]>`	`calculateIntensity(MeshImageStack stack, double thickness)` Thickness is in um.
`ArrayList<double[]>`	`calculateNormalScan(MeshImageStack stack, double thickness)`
`ArrayList<double[]>`	`calculateStress()`
`double`	`calculateVolume()`
`double`	`calculateVolume(double[] dir)`
`void`	`clearEnergies()`
`void`	`confine(Box3D box)`
`void`	`create3DObject()`
`DeformableMesh3D`	`createSubMesh(List<Node3D> nodes)` Creates a mesh consisting of all the provided nodes, and their immediate neighbors.
`Map<Connection3D,Set<Connection3D>>`	`getAdjacencyMap(Map<Node3D,List<Connection3D>> connectionMap)`
`Box3D`	`getBoundingBox()`
`Color`	`getColor()`
`List<Node3D>`	`getConnectedNodes()`
`List<Connection3D>`	`getConnections()`
`double[]`	`getCoordinates(int dex)`
`Map<Node3D,List<Connection3D>>`	`getCurvatureMap()`
`List<ExternalEnergy>`	`getExternalEnergies()`
`List<Connection3D>`	`getOutterBounds()`
`boolean`	`isSelected()`
`boolean`	`isShowSurface()`
`static DeformableMesh3D`	`loadMesh(double[] positions, int[] connection_indices, int[] triangle_indices)`
`Runnable`	`partialUpdate()` Performs the bulk of calculations for doing an update.
`void`	`removeExternalEnergy(ExternalEnergy energy)`
`void`	`resetPositions()`
`void`	`reshape()`
`void`	`rotate(double[] axis, double[] center, double angle)`
`void`	`scale(double v, double[] center)`
`void`	`setColor(Color color)`
`void`	`setPositions(double[] positions)`
`void`	`setSelected(boolean selected)`
`void`	`setShowSurface(boolean showSurface)`
`void`	`syncConnectionIndices()`
`void`	`syncTriangleIndices()`
`void`	`translate(double[] displacement)` Moves all of the nodes in this mesh by the displacement value.
`void`	`update()`
`void`	`updatePositionBuffer(double[] new_data)`

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

Field Detail

GAMMA
```
public double GAMMA
```

ALPHA
```
public double ALPHA
```

BETA
```
public double BETA
```

nodes
```
public List<Node3D> nodes
```

triangles
```
public List<Triangle3D> triangles
```

connections
```
public List<Connection3D> connections
```

positions
```
public double[] positions
```

connection_index
```
public int[] connection_index
```

triangle_index
```
public int[] triangle_index
```

data_object

public DeformableMeshDataObject data_object

ORIGIN
```
public static final double[] ORIGIN
```

Constructor Detail

DeformableMesh3D

public DeformableMesh3D(List<double[]> node_positions,
                        List<int[]> connection_indices,
                        List<int[]> triangle_indices)

Creates a deformable mesh in 3d.

Parameters:: node_positions - collection of double arrays were each array should be {x,y,z}; connection_indices - collection of indexes that indicate connections between nodes.

DeformableMesh3D

public DeformableMesh3D(double[] positions,
                        int[] connection_indices,
                        int[] triangle_indices)

Method Detail

getConnectedNodes

public List<Node3D> getConnectedNodes()

loadMesh

public static DeformableMesh3D loadMesh(double[] positions,
                                        int[] connection_indices,
                                        int[] triangle_indices)

syncConnectionIndices
```
public void syncConnectionIndices()
```

syncTriangleIndices
```
public void syncTriangleIndices()
```

create3DObject
```
public void create3DObject()
```

reshape
```
public void reshape()
```

partialUpdate
```
public Runnable partialUpdate()
```
Performs the bulk of calculations for doing an update. Creates a runnable that represents finally changing the positions

Returns:

update
```
public void update()
```

addExternalEnergy

public void addExternalEnergy(ExternalEnergy energy)

removeExternalEnergy

public void removeExternalEnergy(ExternalEnergy energy)

clearEnergies
```
public void clearEnergies()
```

calculateVolume
```
public double calculateVolume()
```

calculateVolume

public double calculateVolume(double[] dir)

calculateIntensity
```
public ArrayList<double[]> calculateIntensity(MeshImageStack stack,
                                              double thickness)
```
Thickness is in um. The number of steps in will be approximately the number of x pixels in thickness.

Parameters:

stack - source of image data

thickness - thickness to be measured.

Returns:

a list of intensited values along the normal of the triangle. The middle value should be the value

calculateStress

public ArrayList<double[]> calculateStress()

calculateCurvature

public List<double[]> calculateCurvature()

scale

public void scale(double v,
                  double[] center)

rotate

public void rotate(double[] axis,
                   double[] center,
                   double angle)

translate
```
public void translate(double[] displacement)
```
Moves all of the nodes in this mesh by the displacement value.

Parameters:

displacement - xyz displacement values.

calculateNormalScan

public ArrayList<double[]> calculateNormalScan(MeshImageStack stack,
                                               double thickness)

updatePositionBuffer

public void updatePositionBuffer(double[] new_data)

getBoundingBox
```
public Box3D getBoundingBox()
```

getConnections

public List<Connection3D> getConnections()

resetPositions
```
public void resetPositions()
```

setPositions

public void setPositions(double[] positions)

getCoordinates

public double[] getCoordinates(int dex)

getCurvatureMap

public Map<Node3D,List<Connection3D>> getCurvatureMap()

confine
```
public void confine(Box3D box)
```

getAdjacencyMap

public Map<Connection3D,Set<Connection3D>> getAdjacencyMap(Map<Node3D,List<Connection3D>> connectionMap)

setShowSurface

public void setShowSurface(boolean showSurface)

isShowSurface
```
public boolean isShowSurface()
```

setColor
```
public void setColor(Color color)
```

getColor
```
public Color getColor()
```

isSelected
```
public boolean isSelected()
```

setSelected

public void setSelected(boolean selected)

getOutterBounds

public List<Connection3D> getOutterBounds()

getExternalEnergies

public List<ExternalEnergy> getExternalEnergies()

createSubMesh
```
public DeformableMesh3D createSubMesh(List<Node3D> nodes)
```
Creates a mesh consisting of all the provided nodes, and their immediate neighbors. If the mesh is deformed through update, then the neighboring nodes that were added to the sub mesh will be reset to their original position.

Parameters:

nodes - selected nodes that will be deformable in the sub mesh.

Returns:

a new mesh with the selected nodes and any nodes that share an edge or triangle.

Class DeformableMesh3D

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

GAMMA

ALPHA

BETA

nodes

triangles

connections

positions

connection_index

triangle_index

data_object

ORIGIN

Constructor Detail

DeformableMesh3D

DeformableMesh3D

Method Detail

getConnectedNodes

loadMesh

syncConnectionIndices

syncTriangleIndices

create3DObject

reshape

partialUpdate

update

addExternalEnergy

removeExternalEnergy

clearEnergies

calculateVolume

calculateVolume

calculateIntensity

calculateStress

calculateCurvature

scale

rotate

translate

calculateNormalScan

updatePositionBuffer

getBoundingBox

getConnections

resetPositions

setPositions

getCoordinates

getCurvatureMap

confine

getAdjacencyMap

setShowSurface

isShowSurface

setColor

getColor

isSelected

setSelected

getOutterBounds

getExternalEnergies

createSubMesh