org.jmol.shapesurface.Isosurface

All Implemented Interfaces:: MeshDataServer, VertexDataServer

Direct Known Subclasses:: Contact, LcaoCartoon, MolecularOrbital, Pmesh

public class Isosurface extends MeshCollection implements MeshDataServer

Field Summary

Fields

Modifier and Type

Field

Description

protected boolean

iHaveBitSets

protected IsosurfaceMesh[]

isomeshes

int[]

keyXy

protected SurfaceGenerator

sg

protected IsosurfaceMesh

thisMesh

Fields inherited from class org.jmol.shape.MeshCollection
bsDisplay, colix, color, connections, currentMesh, displayWithinDistance2, displayWithinPoints, explicitID, htObjects, isDisplayWithinNot, isFixed, jvxlData, linkedMesh, meshCount, meshes, modelIndex, nUnnamed, pickedMesh, pickedModel, pickedPt, pickedVertex, PREVIOUS_MESH_ID, previousMeshID, title

Fields inherited from class org.jmol.shape.Shape
bsColixSet, bsSizeSet, isBioShape, ms, myType, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr
Constructor Summary

Constructors

Constructor

Description

Isosurface()
Method Summary

Modifier and Type

Method

Description

protected void

addMeshInfo(IsosurfaceMesh mesh, Map<String,Object> info)

void

addRequiredFile(String fileName)

int

addTriangleCheck(int iA, int iB, int iC, int check, int iContour, boolean isAbsolute, int color)

addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)

int

addVertexCopy(T3 vertexXYZ, float value, int assocVertex, boolean asCopy)

addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.

void

allocMesh(String thisID, Mesh m)

P3[]

calculateGeodesicSurface(BS bsSelected, float envelopeRadius)

Map<String,Object>

checkObjectClicked(int x, int y, int action, BS bsVisible, boolean drawPicking)

boolean

checkObjectHovered(int x, int y, BS bsVisible)

protected void

clearSg()

protected void

discardTempData(boolean discardAll)

void

fillMeshData(MeshData meshData, int mode, IsosurfaceMesh mesh)

protected void

getCapSlabInfo(String script)

String

getCmd(int index)

float[]

getPlane(int x)

static String

getPolygonColorData(int ccount, short[] colixes, int[][] polygons, BS bsSlabDisplay)

Object

getProperty(String property, int index)

boolean

getPropertyData(String property, Object[] data)

protected Object

getPropI(String property, int index)

Object

getShapeDetail()

String

getShapeState()

int

getSurfacePointIndexAndFraction(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, P3i offset, int vA, int vB, float valueA, float valueB, T3 pointA, V3 edgeVector, boolean isContourType, float[] fReturn)

getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.

float

getValue(int x, int y, int z, int ptyz)

for readers only

protected Object

getValues(Mesh mesh)

protected Object

getVertices(Mesh mesh)

void

initShape()

void

invalidateTriangles()

protected void

newSg()

boolean

notifySurfaceGenerationCompleted()

void

notifySurfaceMappingCompleted()

void

setOutputChannel(GenericBinaryDocument binaryDoc, OC out)

void

setProperty(String propertyName, Object value, BS bs)

protected void

setPropI(String propertyName, Object value, BS bs)

void

setRequiredFile(String oldName, String fileName)

protected void

setScriptInfo(String strCommand)

protected void

slabPolygons(Object[] slabInfo)

Methods inherited from class org.jmol.shape.MeshCollection
checkExplicit, clean, deleteMeshI, deleteMeshKey, getIndexFromName, getMesh, getMeshList, getPickedPoint, getPropDataMC, getPropMC, merge, resetObjects, setMeshColor, setModelVisibilityFlags, setPropMC, setStatusPicked, setTitle, setTokenProperty

Methods inherited from class org.jmol.shape.Shape
appendCmd, checkBoundsMinMax, checkObjectDragged, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColixA, getColixB, getColixI, getColorCommand, getColorCommandUnk, getFontCommand, getPropShape, getSize, getSizeG, getTranslucentLabel, initializeShape, initModelSet, replaceGroup, setAtomClickability, setModelSet, setProperties, setPropS, setShapeSizeRD, setSize, setSizeRD, wasClicked

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

Field Details
- isomeshes
  
  protected IsosurfaceMesh[] isomeshes
- thisMesh
  
  protected IsosurfaceMesh thisMesh
- iHaveBitSets
  
  protected boolean iHaveBitSets
- sg
  
  protected SurfaceGenerator sg
- keyXy
  
  public int[] keyXy
Constructor Details
- Isosurface
  
  public Isosurface()
Method Details
- allocMesh
  
  public void allocMesh(String thisID, Mesh m)
  
  Overrides:
  
  allocMesh in class MeshCollection
- initShape
  
  public void initShape()
  
  Overrides:
  
  initShape in class MeshCollection
- newSg
  
  protected void newSg()
- clearSg
  
  protected void clearSg()
- setProperty
  
  public void setProperty(String propertyName, Object value, BS bs)
  
  Specified by:
  
  setProperty in class Shape
- setPropI
  
  protected void setPropI(String propertyName, Object value, BS bs)
- slabPolygons
  
  protected void slabPolygons(Object[] slabInfo)
- getPropertyData
  
  public boolean getPropertyData(String property, Object[] data)
  
  Overrides:
  
  getPropertyData in class Shape
  
  Parameters:
  
  property -
  
  data -
  
  Returns:
  
  true if serviced
- getProperty
  
  public Object getProperty(String property, int index)
  
  Overrides:
  
  getProperty in class Shape
  
  Parameters:
  
  property -
  
  index -
  
  Returns:
  
  true if serviced
- getPropI
  
  protected Object getPropI(String property, int index)
- getPolygonColorData
  
  public static String getPolygonColorData(int ccount, short[] colixes, int[][] polygons, BS bsSlabDisplay)
- getShapeState
  
  public String getShapeState()
  
  Specified by:
  
  getShapeState in class Shape
- getCapSlabInfo
  
  protected void getCapSlabInfo(String script)
- discardTempData
  
  protected void discardTempData(boolean discardAll)
- invalidateTriangles
  
  public void invalidateTriangles()
  
  Specified by:
  
  invalidateTriangles in interface MeshDataServer
- setOutputChannel
  
  public void setOutputChannel(GenericBinaryDocument binaryDoc, OC out)
  
  Specified by:
  
  setOutputChannel in interface MeshDataServer
- fillMeshData
  
  public void fillMeshData(MeshData meshData, int mode, IsosurfaceMesh mesh)
  
  Specified by:
  
  fillMeshData in interface MeshDataServer
- notifySurfaceGenerationCompleted
  
  public boolean notifySurfaceGenerationCompleted()
  
  Specified by:
  
  notifySurfaceGenerationCompleted in interface MeshDataServer
- notifySurfaceMappingCompleted
  
  public void notifySurfaceMappingCompleted()
  
  Specified by:
  
  notifySurfaceMappingCompleted in interface MeshDataServer
- calculateGeodesicSurface
  
  public P3[] calculateGeodesicSurface(BS bsSelected, float envelopeRadius)
  
  Specified by:
  
  calculateGeodesicSurface in interface MeshDataServer
- getSurfacePointIndexAndFraction
  
  public int getSurfacePointIndexAndFraction(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, P3i offset, int vA, int vB, float valueA, float valueB, T3 pointA, V3 edgeVector, boolean isContourType, float[] fReturn)
  
  Description copied from interface: VertexDataServer
  
  getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge. If a vertex is discarded, then Integer.MAX_VALUE should be returned. the 3D coordinate of the point can be calculated using surfacePoint.scaleAdd(fraction, edgeVector, pointA); where fraction is generally calculated as: fraction = (cutoff - valueA) / (valueB - valueA); if (isCutoffAbsolute invalid input: '&'invalid input: '&' (fraction invalid input: '<' 0 || fraction > 1)) fraction = (-cutoff - valueA) / (valueB - valueA); This method is also used by MarchingCubes to deliver the appropriate oblique planar coordinate to MarchingSquares for later contouring.
  
  Specified by:
  
  getSurfacePointIndexAndFraction in interface VertexDataServer
  
  Parameters:
  
  cutoff -
  
  isCutoffAbsolute -
  
  x -
  
  y -
  
  z -
  
  offset -
  
  vA - [0:7]
  
  vB - [0:7]
  
  valueA -
  
  valueB -
  
  pointA -
  
  edgeVector - vector from A to B
  
  isContourType -
  
  fReturn -
  
  Returns:
  
  new vertex index or Integer.MAX_VALUE
- addVertexCopy
  
  public int addVertexCopy(T3 vertexXYZ, float value, int assocVertex, boolean asCopy)
  
  Description copied from interface: VertexDataServer
  
  addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane. The implementing method should COPY the Point3f using Point3f.set(). The data consumer can use the association key to group this vertex with others near the same gridpoint.
  
  Specified by:
  
  addVertexCopy in interface VertexDataServer
  
  Parameters:
  
  vertexXYZ -
  
  value -
  
  assocVertex - unique association vertex or -1
  
  asCopy -
  
  Returns:
  
  new vertex index
- addTriangleCheck
  
  public int addTriangleCheck(int iA, int iB, int iC, int check, int iContour, boolean isAbsolute, int color)
  
  Description copied from interface: VertexDataServer
  
  addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
  
  Specified by:
  
  addTriangleCheck in interface VertexDataServer
  
  Parameters:
  
  iA -
  
  iB -
  
  iC -
  
  check -
  
  iContour - TODO
  
  isAbsolute -
  
  color -
  
  Returns:
  
  polygon index or -1
- setScriptInfo
  
  protected void setScriptInfo(String strCommand)
- addRequiredFile
  
  public void addRequiredFile(String fileName)
  
  Specified by:
  
  addRequiredFile in interface MeshDataServer
- setRequiredFile
  
  public void setRequiredFile(String oldName, String fileName)
  
  Specified by:
  
  setRequiredFile in interface MeshDataServer
- getShapeDetail
  
  public Object getShapeDetail()
  
  Overrides:
  
  getShapeDetail in class Shape
- addMeshInfo
  
  protected void addMeshInfo(IsosurfaceMesh mesh, Map<String,Object> info)
- getPlane
  
  public float[] getPlane(int x)
  
  Specified by:
  
  getPlane in interface VertexDataServer
- getValue
  
  public float getValue(int x, int y, int z, int ptyz)
  
  Description copied from interface: VertexDataServer
  
  for readers only
  
  Specified by:
  
  getValue in interface VertexDataServer
  
  Parameters:
  
  x -
  
  y -
  
  z -
  
  ptyz -
  
  Returns:
  
  value[x][y][z]
- checkObjectHovered
  
  public boolean checkObjectHovered(int x, int y, BS bsVisible)
  
  Overrides:
  
  checkObjectHovered in class Shape
  
  Parameters:
  
  x -
  
  y -
  
  bsVisible -
  
  Returns:
  
  T/F
- checkObjectClicked
  
  public Map<String,Object> checkObjectClicked(int x, int y, int action, BS bsVisible, boolean drawPicking)
  
  Overrides:
  
  checkObjectClicked in class Shape
  
  Parameters:
  
  x -
  
  y -
  
  action -
  
  bsVisible -
  
  drawPicking - TODO
  
  Returns:
  
  Hashtable containing information about pt clicked
- getCmd
  
  public String getCmd(int index)
- getValues
  
  protected Object getValues(Mesh mesh)
  
  Overrides:
  
  getValues in class MeshCollection
- getVertices
  
  protected Object getVertices(Mesh mesh)
  
  Overrides:
  
  getVertices in class MeshCollection

Class Isosurface

Field Summary

Fields inherited from class org.jmol.shape.MeshCollection

Fields inherited from class org.jmol.shape.Shape

Constructor Summary

Method Summary

Methods inherited from class org.jmol.shape.MeshCollection

Methods inherited from class org.jmol.shape.Shape

Methods inherited from class java.lang.Object

Field Details

isomeshes

thisMesh

iHaveBitSets

sg

keyXy

Constructor Details

Isosurface

Method Details

allocMesh

initShape

newSg

clearSg

setProperty

setPropI

slabPolygons

getPropertyData

getProperty

getPropI

getPolygonColorData

getShapeState

getCapSlabInfo

discardTempData

invalidateTriangles

setOutputChannel

fillMeshData

notifySurfaceGenerationCompleted

notifySurfaceMappingCompleted

calculateGeodesicSurface

getSurfacePointIndexAndFraction

addVertexCopy

addTriangleCheck

setScriptInfo

addRequiredFile

setRequiredFile

getShapeDetail

addMeshInfo

getPlane

getValue

checkObjectHovered

checkObjectClicked

getCmd

getValues

getVertices