org.jmol.shapesurface

Class Isosurface

java.lang.Object

org.jmol.shape.Shape

org.jmol.shape.MeshCollection

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 and Description
private java.lang.String	actualID
(package private) boolean	allowMesh
private boolean	associateNormals
private int	atomIndex
private javax.vecmath.Point3f	center
private float[]	cutoffRange
private short	defaultColix
private boolean	explicitContours
protected boolean	iHaveBitSets
private boolean	iHaveModelIndex
private boolean	isColorExplicit
private IsosurfaceMesh[]	isomeshes
private boolean	isPhaseColored
private boolean	isWithinNot
protected JvxlData	jvxlData
(package private) int[]	keyXy
private javax.vecmath.Point4f	lcaoDir
private static int	MAX_OBJECT_CLICK_DISTANCE_SQUARED
private short	meshColix
private float[]	moLinearCombination
private int	moNumber
private int	nLCAO
private javax.vecmath.Point3f	offset
private double	privateKey
private javax.vecmath.Point3i	ptXY
private float	scale3d
private java.lang.String	script
private java.lang.String	scriptAppendix
protected SurfaceGenerator	sg
protected IsosurfaceMesh	thisMesh
private float	withinDistance2
private java.util.List<javax.vecmath.Point3f>	withinPoints

Fields inherited from class org.jmol.shape.MeshCollection

bsDisplay, colix, color, connections, currentMesh, displayWithinDistance2, displayWithinPoints, explicitID, htObjects, isDisplayWithinNot, isFixed, linkedMesh, meshCount, meshes, modelIndex, myType, nUnnamed, pickedMesh, pickedModel, pickedVertex, PREVIOUS_MESH_ID, previousMeshID, title

Fields inherited from class org.jmol.shape.Shape

g3d, isBioShape, modelSet, myVisibilityFlag, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, viewer, xmlProperties

Constructor Summary

Constructors

Constructor and Description
Isosurface()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	addMeshInfo(IsosurfaceMesh mesh, java.util.Map<java.lang.String,java.lang.Object> info)
void	addRequiredFile(java.lang.String fileName)
int	addTriangleCheck(int iA, int iB, int iC, int check, int check2, 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(javax.vecmath.Point3f vertexXYZ, float value, int assocVertex) 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(java.lang.String thisID, Mesh m)
javax.vecmath.Point3f[]	calculateGeodesicSurface(java.util.BitSet bsSelected, float envelopeRadius)
private java.lang.Object	calculateVolumeOrArea(boolean isArea)
java.util.Map<java.lang.String,java.lang.Object>	checkObjectClicked(int x, int y, int action, java.util.BitSet bsVisible)
boolean	checkObjectHovered(int x, int y, java.util.BitSet bsVisible)
protected void	clearSg()
private void	createLcaoLobe(javax.vecmath.Vector3f lobeAxis, float factor, int nElectrons)
protected void	discardTempData(boolean discardAll)
private void	drawLcaoCartoon(javax.vecmath.Vector3f z, javax.vecmath.Vector3f x, javax.vecmath.Vector3f rotAxis, int nElectrons)
void	fillMeshData(MeshData meshData, int mode, IsosurfaceMesh mesh)
private java.lang.String	findValue(int x, int y, boolean isPicking, java.util.BitSet bsVisible)
protected void	getCapSlabInfo(java.lang.String script)
private boolean	getClosestNormal(IsosurfaceMesh m, javax.vecmath.Point3f toPt, javax.vecmath.Point3f ptRet, javax.vecmath.Vector3f normalRet)
private void	getClosestPoint(IsosurfaceMesh m, int imin, javax.vecmath.Point3f toPt, javax.vecmath.Point3f ptRet, javax.vecmath.Vector3f normalRet)
java.lang.String	getCmd(int index)
private short	getDefaultColix()
private void	getMeshCommand(java.lang.StringBuffer sb, int i)
float[]	getPlane(int x)
static java.lang.String	getPolygonColorData(int ccount, short[] colixes, java.util.BitSet bsSlabDisplay)
java.lang.Object	getProperty(java.lang.String property, int index)
boolean	getProperty(java.lang.String property, java.lang.Object[] data)
private boolean	getScriptBitSets(java.lang.String script, java.util.BitSet[] bsCmd)
java.util.List<java.util.Map<java.lang.String,java.lang.Object>>	getShapeDetail()
java.lang.String	getShapeState()
int	getSurfacePointIndexAndFraction(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, javax.vecmath.Point3i offset, int vA, int vB, float valueA, float valueB, javax.vecmath.Point3f pointA, javax.vecmath.Vector3f 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
private void	hoverKey(int x, int y)
private void	initializeIsosurface()
void	initShape()
private void	initState()
void	invalidateTriangles()
private boolean	isPickable(IsosurfaceMesh m, java.util.BitSet bsVisible)
void	merge(Shape shape) called by ParallelProcessor at completion
private void	navigate(int dz)
protected void	newSg()
void	notifySurfaceGenerationCompleted()
void	notifySurfaceMappingCompleted()
private void	setBsVdw()
private void	setHeading(javax.vecmath.Point3f pt, javax.vecmath.Vector3f vNorm, int nSeconds)
private void	setJvxlInfo()
private void	setMesh()
void	setOutputStream(BinaryDocument binaryDoc, java.io.OutputStream os)
void	setProperty(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs) may come from any source -- executed AFTER a shape's own setProperty method
private void	setPropertySuper(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs)
protected void	setScriptInfo(java.lang.String strCommand)
protected void	slabPolygons(java.lang.Object[] slabInfo)

Methods inherited from class org.jmol.shape.MeshCollection

checkExplicit, clean, deleteMesh, deleteMesh, getIndexFromName, getMesh, getPickedPoint, setStatusPicked, setVisibilityFlags

Methods inherited from class org.jmol.shape.Shape

appendCmd, checkBoundsMinMax, checkObjectDragged, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColorCommand, getColorCommand, getFontCommand, getShapeCommands, getShapeCommands, getSize, getSize, getTranslucentLabel, getViewer, initializeShape, initModelSet, setColix, setColix, setColix, setModelClickability, setModelSet, setShapeProperty, setShapeSize, setSize, setSize, setStateInfo, setStateInfo, wasClicked

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

defaultColix

private short defaultColix

meshColix

private short meshColix

center

private javax.vecmath.Point3f center

offset

private javax.vecmath.Point3f offset

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 java.util.List<javax.vecmath.Point3f> withinPoints

cutoffRange

private float[] cutoffRange

allowMesh

boolean allowMesh

script

private java.lang.String script

iHaveModelIndex

private boolean iHaveModelIndex

nLCAO

private int nLCAO

lcaoDir

private javax.vecmath.Point4f lcaoDir

privateKey

private double privateKey

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 javax.vecmath.Point3i ptXY

keyXy

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,
               java.util.BitSet bs)

Description copied from class: Shape

may come from any source -- executed AFTER a shape's own setProperty method

Overrides:

setProperty in class MeshCollection

slabPolygons

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

setPropertySuper

private void setPropertySuper(java.lang.String propertyName,
                    java.lang.Object value,
                    java.util.BitSet bs)

getProperty

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

Overrides:

getProperty in class MeshCollection

Returns:

true if serviced

getProperty

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

Overrides:

getProperty in class MeshCollection

Returns:

true if serviced

calculateVolumeOrArea

private java.lang.Object calculateVolumeOrArea(boolean isArea)

getPolygonColorData

public static java.lang.String getPolygonColorData(int ccount,
                                   short[] colixes,
                                   java.util.BitSet bsSlabDisplay)

getShapeState

public java.lang.String getShapeState()

Overrides:

getShapeState in class Shape

getMeshCommand

private void getMeshCommand(java.lang.StringBuffer sb,
                  int i)

getScriptBitSets

private boolean getScriptBitSets(java.lang.String script,
                       java.util.BitSet[] bsCmd)

getCapSlabInfo

protected void getCapSlabInfo(java.lang.String script)

initializeIsosurface

private void initializeIsosurface()

initState

private void initState()

setMesh

private void setMesh()

discardTempData

protected void discardTempData(boolean discardAll)

getDefaultColix

private short getDefaultColix()

drawLcaoCartoon

private void drawLcaoCartoon(javax.vecmath.Vector3f z,
                   javax.vecmath.Vector3f x,
                   javax.vecmath.Vector3f rotAxis,
                   int nElectrons)

createLcaoLobe

private void createLcaoLobe(javax.vecmath.Vector3f lobeAxis,
                  float factor,
                  int nElectrons)

invalidateTriangles

public void invalidateTriangles()

Specified by:

invalidateTriangles in interface MeshDataServer

setOutputStream

public void setOutputStream(BinaryDocument binaryDoc,
                   java.io.OutputStream os)

Specified by:

setOutputStream in interface MeshDataServer

fillMeshData

public void fillMeshData(MeshData meshData,
                int mode,
                IsosurfaceMesh mesh)

Specified by:

fillMeshData in interface MeshDataServer

notifySurfaceGenerationCompleted

public void notifySurfaceGenerationCompleted()

Specified by:

notifySurfaceGenerationCompleted in interface MeshDataServer

notifySurfaceMappingCompleted

public void notifySurfaceMappingCompleted()

Specified by:

notifySurfaceMappingCompleted in interface MeshDataServer

setBsVdw

private void setBsVdw()

calculateGeodesicSurface

public javax.vecmath.Point3f[] calculateGeodesicSurface(java.util.BitSet bsSelected,
                                               float envelopeRadius)

Specified by:

calculateGeodesicSurface in interface MeshDataServer

getSurfacePointIndexAndFraction

public int getSurfacePointIndexAndFraction(float cutoff,
                                  boolean isCutoffAbsolute,
                                  int x,
                                  int y,
                                  int z,
                                  javax.vecmath.Point3i offset,
                                  int vA,
                                  int vB,
                                  float valueA,
                                  float valueB,
                                  javax.vecmath.Point3f pointA,
                                  javax.vecmath.Vector3f 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(javax.vecmath.Point3f vertexXYZ,
                float value,
                int assocVertex)

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 check2,
                   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

check2 - 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.util.List<java.util.Map<java.lang.String,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,
                         java.util.BitSet 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,
                                                                  java.util.BitSet bsVisible)

Overrides:

checkObjectClicked in class Shape

Returns:

Hashtable containing information about pt clicked

isPickable

private boolean isPickable(IsosurfaceMesh m,
                 java.util.BitSet bsVisible)

navigate

private void navigate(int dz)

setHeading

private void setHeading(javax.vecmath.Point3f pt,
              javax.vecmath.Vector3f vNorm,
              int nSeconds)

getClosestNormal

private boolean getClosestNormal(IsosurfaceMesh m,
                       javax.vecmath.Point3f toPt,
                       javax.vecmath.Point3f ptRet,
                       javax.vecmath.Vector3f normalRet)

getClosestPoint

private void getClosestPoint(IsosurfaceMesh m,
                   int imin,
                   javax.vecmath.Point3f toPt,
                   javax.vecmath.Point3f ptRet,
                   javax.vecmath.Vector3f normalRet)

findValue

private java.lang.String findValue(int x,
                         int y,
                         boolean isPicking,
                         java.util.BitSet bsVisible)

Parameters:

x -

y -

isPicking - IGNORED

bsVisible -

Returns:

value found

merge

public void merge(Shape shape)

Description copied from class: MeshCollection

called by ParallelProcessor at completion

Overrides:

merge in class MeshCollection

getCmd

public java.lang.String getCmd(int index)