Field Detail

• isomeshes

  private IsosurfaceMesh[] isomeshes

• thisMesh

  protected IsosurfaceMesh thisMesh

• actualID

  private java.lang.String actualID

• iHaveBitSets

  protected boolean iHaveBitSets

• explicitContours

  private boolean explicitContours

• atomIndex

  private int atomIndex

• moNumber

  private int moNumber

• moLinearCombination

  private float[] moLinearCombination

• colorType

  private int colorType

• defaultColix

  private short defaultColix

• meshColix

  private short meshColix

• center

  private javajs.util.P3 center

• scale3d

  private float scale3d

• isPhaseColored

  private boolean isPhaseColored

• isColorExplicit

  private boolean isColorExplicit

• scriptAppendix

  private java.lang.String scriptAppendix

• sg

  protected SurfaceGenerator sg

• jvxlData

  protected JvxlData jvxlData

• withinDistance2

  private float withinDistance2

• isWithinNot

  private boolean isWithinNot

• withinPoints

  private javajs.util.Lst<javajs.util.P3> withinPoints

• cutoffRange

  private float[] cutoffRange

• allowMesh

  boolean allowMesh

• script

  private java.lang.String script

• iHaveModelIndex

  private boolean iHaveModelIndex

• nLCAO

  private int nLCAO

• lcaoDir

  private javajs.util.P4 lcaoDir

• associateNormals

  private boolean associateNormals

• MAX_OBJECT_CLICK_DISTANCE_SQUARED

  private static final int MAX_OBJECT_CLICK_DISTANCE_SQUARED

  See Also:

  Constant Field Values

• ptXY

  private final javajs.util.P3i ptXY

• keyXy

  public int[] keyXy

Constructor Detail

• Isosurface

  public Isosurface()

Method Detail

• allocMesh

  public void allocMesh​(java.lang.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​(java.lang.String propertyName,
                          java.lang.Object value,
                          BS bs)

  Specified by:

  setProperty in class Shape

• setPropI

  protected void setPropI​(java.lang.String propertyName,
                          java.lang.Object value,
                          BS bs)

• setIsoMeshColor

  private void setIsoMeshColor​(IsosurfaceMesh m,
                               java.lang.String color)

• setColorPhase

  private void setColorPhase​(IsosurfaceMesh m,
                             short colix0,
                             short colix1)

• ensureMeshSource

  private void ensureMeshSource()

• slabPolygons

  protected void slabPolygons​(java.lang.Object[] slabInfo)

• setPropertySuper

  private void setPropertySuper​(java.lang.String propertyName,
                                java.lang.Object value,
                                BS bs)

• getPropertyData

  public boolean getPropertyData​(java.lang.String property,
                                 java.lang.Object[] data)

  Overrides:

  getPropertyData in class Shape

  Returns:

  true if serviced

• getProperty

  public java.lang.Object getProperty​(java.lang.String property,
                                      int index)

  Overrides:

  getProperty in class Shape

  Returns:

  true if serviced

• getPropI

  protected java.lang.Object getPropI​(java.lang.String property,
                                      int index)

• getDataRange

  private float[] getDataRange​(IsosurfaceMesh mesh)

• calculateVolumeOrArea

  private java.lang.Object calculateVolumeOrArea​(IsosurfaceMesh mesh,
                                                 boolean isArea)

• getPolygonColorData

  public static java.lang.String getPolygonColorData​(int ccount,
                                                     short[] colixes,
                                                     int[][] polygons,
                                                     BS bsSlabDisplay)

• getShapeState

  public java.lang.String getShapeState()

  Specified by:

  getShapeState in class Shape

• getMeshCommand

  private void getMeshCommand​(javajs.util.SB sb,
                              int i)

• getScriptBitSets

  private boolean getScriptBitSets​(java.lang.String script,
                                   BS[] bsCmd)

• getCapSlabInfo

  protected void getCapSlabInfo​(java.lang.String script)

• getCapSlabObject

  private java.lang.Object[] getCapSlabObject​(java.lang.String s,
                                              boolean isCap)

  legacy -- for some scripts with early isosurface slabbing

  Parameters:

  s -

  isCap -

  Returns:

  slabInfo object

• initializeIsosurface

  private void initializeIsosurface()

• initState

  private void initState()

• setMeshI

  private void setMeshI()

• discardTempData

  protected void discardTempData​(boolean discardAll)

• getDefaultColix

  private short getDefaultColix()

• drawLcaoCartoon

  private void drawLcaoCartoon​(javajs.util.V3 z,
                               javajs.util.V3 x,
                               javajs.util.V3 rotAxis,
                               int nElectrons)

• createLcaoLobe

  private void createLcaoLobe​(javajs.util.V3 lobeAxis,
                              float factor,
                              int nElectrons)

• invalidateTriangles

  public void invalidateTriangles()

  Specified by:

  invalidateTriangles in interface MeshDataServer

• setOutputChannel

  public void setOutputChannel​(javajs.api.GenericBinaryDocument binaryDoc,
                               javajs.util.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

• setBsVdw

  private void setBsVdw()

• calculateGeodesicSurface

  public javajs.util.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,
                                             javajs.util.P3i offset,
                                             int vA,
                                             int vB,
                                             float valueA,
                                             float valueB,
                                             javajs.util.T3 pointA,
                                             javajs.util.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 && (fraction < 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

  vA - [0:7]

  vB - [0:7]

  edgeVector - vector from A to B

  Returns:

  new vertex index or Integer.MAX_VALUE

• addVertexCopy

  public int addVertexCopy​(javajs.util.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

  assocVertex - unique association vertex or -1

  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

  iContour - TODO

  Returns:

  polygon index or -1

• setScriptInfo

  protected void setScriptInfo​(java.lang.String strCommand)

• addRequiredFile

  public void addRequiredFile​(java.lang.String fileName)

  Specified by:

  addRequiredFile in interface MeshDataServer

• setJvxlInfo

  private void setJvxlInfo()

• getShapeDetail

  public java.lang.Object getShapeDetail()

  Overrides:

  getShapeDetail in class Shape

• addMeshInfo

  protected void addMeshInfo​(IsosurfaceMesh mesh,
                             java.util.Map<java.lang.String,​java.lang.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

  Returns:

  value[x][y][z]

• checkObjectHovered

  public boolean checkObjectHovered​(int x,
                                    int y,
                                    BS bsVisible)

  Overrides:

  checkObjectHovered in class Shape

  Returns:

  T/F

• hoverKey

  private void hoverKey​(int x,
                        int y)

• checkObjectClicked

  public java.util.Map<java.lang.String,​java.lang.Object> checkObjectClicked​(int x,
                                                                                   int y,
                                                                                   int action,
                                                                                   BS bsVisible,
                                                                                   boolean drawPicking)

  Overrides:

  checkObjectClicked in class Shape

  drawPicking - TODO

  Returns:

  Hashtable containing information about pt clicked

• isPickable

  private boolean isPickable​(IsosurfaceMesh m,
                             BS bsVisible)

• findValue

  private java.lang.String findValue​(int x,
                                     int y,
                                     boolean isPicking,
                                     BS bsVisible)

  Parameters:

  x -

  y -

  isPicking - IGNORED

  bsVisible -

  Returns:

  value found

• getCmd

  public java.lang.String getCmd​(int index)