Package org.jmol.jvxl.data
Class JvxlCoder
java.lang.Object
org.jmol.jvxl.data.JvxlCoder
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate static void
static void
appendContourTriangleIntersection
(int type, float f1, float f2, javajs.util.SB fData) appends an integer (3, 5, or 6) representing two sides of a triangle ABC -- AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges for the intersection point base-90-encoded.private static void
appendEncodedBitSetTag
(javajs.util.SB sb, String name, javajs.util.BS bs, int count, Object[] attribs) private static void
appendXmlColorData
(javajs.util.SB sb, String data, boolean isEncoded, boolean isPrecisionColor, float value1, float value2) private static void
appendXmlEdgeData
(javajs.util.SB sb, JvxlData jvxlData) private static boolean
appendXmlTriangleData
(javajs.util.SB sb, int[][] triangles, int nData, javajs.util.BS bsSlabDisplay, int[] vertexIdNew, boolean escapeXml) encode triangle data -- [ia ib ic] [ia ib ic] [ia ib ic] ...private static void
appendXmlVertexData
(javajs.util.SB sb, JvxlData jvxlData, int[] vertexIdNew, javajs.util.T3[] vertices, float[] vertexValues, int vertexCount, String polygonColorData, int polygonCount, javajs.util.BS bsSlabDisplay, int[] vertexColors, boolean addColorData, boolean escapeXml) encode the vertex data.private static void
appendXmlVertexOnlyData
(javajs.util.SB sb, JvxlData jvxlData, MeshData meshData, boolean escapeXml) private static void
private static javajs.util.T3
getContourPoint
(javajs.util.T3[] vertices, int i, int j, float f) private static void
jvxlAppendCharacter2
(float value, float min, float max, int base, int range, javajs.util.SB list1, javajs.util.SB list2) private static void
jvxlAppendCommandState
(javajs.util.SB data, String cmd, String state) static void
jvxlAppendEncodedNumber
(javajs.util.SB sb, int n, int base, int range) static String
jvxlCompressString
(String data, boolean escapeXml) static void
jvxlCreateColorData
(JvxlData jvxlData, float[] vertexValues) static void
jvxlCreateHeader
(VolumeData v, javajs.util.SB sb) Creates a two-line header for the XJVXL file.static void
jvxlCreateHeaderWithoutTitleOrAtoms
(VolumeData v, javajs.util.SB bs) static javajs.util.BS
jvxlDecodeBitSet
(String data) static javajs.util.BS
jvxlDecodeBitSetRange
(String data, int base, int range) static String
jvxlDecompressString
(String data) static String
jvxlEncodeBitSet
(javajs.util.BS bs) static int
jvxlEncodeBitSet0
(javajs.util.BS bs, int nPoints, javajs.util.SB sb) static int
jvxlEncodeBitSetBuffer
(javajs.util.BS bs, int nPoints, javajs.util.SB sb) private static void
jvxlEncodeContourData
(javajs.util.Lst<Object>[] contours, javajs.util.SB sb) contour data are appended to a string buffer in the form of atriangle bitset data triangle bitset data triangle bitset data ...static char
jvxlFractionAsCharacter
(float fraction) static char
jvxlFractionAsCharacterRange
(float fraction, int base, int range) static float
jvxlFractionFromCharacter
(int ich, int base, int range, float fracOffset) static float
jvxlFractionFromCharacter2
(int ich1, int ich2, int base, int range) static String
jvxlGetFile
(JvxlData jvxlData, MeshData meshData, String[] title, String msg, boolean includeHeader, int nSurfaces, String state, String comment) static String
jvxlGetFile
(VolumeData volumeData, JvxlData jvxlData, String[] title) static String
jvxlGetInfo
(JvxlData jvxlData) static String
jvxlGetInfoData
(JvxlData jvxlData, boolean vertexDataOnly) static int
jvxlParseEncodedInt
(String str, int offset, int base, int[] next) private static String
jvxlSetCompressionRatio
(javajs.util.SB data, JvxlData jvxlData, int len) static char
jvxlValueAsCharacter
(float value, float min, float max, int base, int range) protected static float
jvxlValueFromCharacter2
(int ich, int ich2, float min, float max, int base, int range) static void
set3dContourVector
(javajs.util.Lst<Object> v, int[][] polygonIndexes, javajs.util.T3[] vertices) Interpret fractional data in terms of actual vertex positions and create the elements of a Vector in Vector[] vContours starting at the CONTOUR_POINTS position.private static String
subsetString
(javajs.util.BS bs)
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Field Details
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JVXL_VERSION1
- See Also:
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JVXL_VERSION_XML
- See Also:
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haveXMLUtil
private static boolean haveXMLUtil -
CONTOUR_NPOLYGONS
public static final int CONTOUR_NPOLYGONS- See Also:
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CONTOUR_BITSET
public static final int CONTOUR_BITSET- See Also:
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CONTOUR_VALUE
public static final int CONTOUR_VALUE- See Also:
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CONTOUR_COLIX
public static final int CONTOUR_COLIX- See Also:
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CONTOUR_COLOR
public static final int CONTOUR_COLOR- See Also:
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CONTOUR_FDATA
public static final int CONTOUR_FDATA- See Also:
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CONTOUR_POINTS
public static final int CONTOUR_POINTS- See Also:
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defaultEdgeFractionBase
public static final int defaultEdgeFractionBase- See Also:
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defaultEdgeFractionRange
public static final int defaultEdgeFractionRange- See Also:
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defaultColorFractionBase
public static final int defaultColorFractionBase- See Also:
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defaultColorFractionRange
public static final int defaultColorFractionRange- See Also:
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Constructor Details
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JvxlCoder
public JvxlCoder()
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Method Details
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jvxlGetFile
- Parameters:
volumeData
-jvxlData
-title
-- Returns:
- XML string
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jvxlGetFile
public static String jvxlGetFile(JvxlData jvxlData, MeshData meshData, String[] title, String msg, boolean includeHeader, int nSurfaces, String state, String comment) - Parameters:
jvxlData
-meshData
-title
-msg
-includeHeader
-nSurfaces
-state
-comment
-- Returns:
- JVXL file XML
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checkHaveXMLUtil
private static void checkHaveXMLUtil() -
appendEncodedBitSetTag
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jvxlSetCompressionRatio
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appendXmlEdgeData
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jvxlAppendCommandState
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appendXmlColorData
private static void appendXmlColorData(javajs.util.SB sb, String data, boolean isEncoded, boolean isPrecisionColor, float value1, float value2) -
jvxlGetInfo
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jvxlGetInfoData
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subsetString
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addAttrib
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jvxlEncodeContourData
contour data are appended to a string buffer in the form of atriangle bitset data triangle bitset data triangle bitset data ...- Parameters:
contours
-sb
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set3dContourVector
public static void set3dContourVector(javajs.util.Lst<Object> v, int[][] polygonIndexes, javajs.util.T3[] vertices) Interpret fractional data in terms of actual vertex positions and create the elements of a Vector in Vector[] vContours starting at the CONTOUR_POINTS position.- Parameters:
v
-polygonIndexes
-vertices
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getContourPoint
private static javajs.util.T3 getContourPoint(javajs.util.T3[] vertices, int i, int j, float f) -
appendContourTriangleIntersection
public static void appendContourTriangleIntersection(int type, float f1, float f2, javajs.util.SB fData) appends an integer (3, 5, or 6) representing two sides of a triangle ABC -- AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges for the intersection point base-90-encoded. This version is single precision. type f1 f2 3 AB BC 5 AB CA 6 BC CA- Parameters:
type
-f1
- -- character-encoded fractionf2
- -- character-encoded fractionfData
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jvxlCreateColorData
- Parameters:
jvxlData
-vertexValues
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appendXmlVertexOnlyData
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appendXmlTriangleData
private static boolean appendXmlTriangleData(javajs.util.SB sb, int[][] triangles, int nData, javajs.util.BS bsSlabDisplay, int[] vertexIdNew, boolean escapeXml) encode triangle data -- [ia ib ic] [ia ib ic] [ia ib ic] ... algorithm written by Bob Hanson, 11/2008. The principle is that not all vertices may be represented -- we only need the used vertices here. Capitalizing on the fact that triangle sets tend to have common edges and similar numbers for sequential triangles. a) Renumbering vertices as they appear in the triangle set [2456 2457 2458] [2456 2459 2458] becomes [ 1 2 3] [ 1 4 3] b) This allows efficient encoding of differences, not absolute numbers. 0 1 2 -2 3 -1 c) Which can then be represented often using a single ASCII character. I chose \ to be 0, and replace that with !. ASCII: -30 -20 -10 0 +10 +20 +30 <=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{| So the above sequence would simply be: !]^Z_[ When the range falls outside of +/-32, we simply use a number. When a positive number follows another number, we add a "+" to it. !]^Z_[-33+250]230-210]] Preliminary trials indicated that on average a triangle can be encoded in about 7 bytes, or roughly half the 12 bytes necessary for standard binary encoding of integers. The advantage here is that we have an ASCII-readable file and no little-/big-endian issue.- Parameters:
sb
-triangles
-nData
-bsSlabDisplay
-vertexIdNew
-escapeXml
-- Returns:
- (triangles are present)
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appendXmlVertexData
private static void appendXmlVertexData(javajs.util.SB sb, JvxlData jvxlData, int[] vertexIdNew, javajs.util.T3[] vertices, float[] vertexValues, int vertexCount, String polygonColorData, int polygonCount, javajs.util.BS bsSlabDisplay, int[] vertexColors, boolean addColorData, boolean escapeXml) encode the vertex data. This must be done AFTER encoding the triangles, because the triangles redefine the order of vertices. Bob Hanson 11/2008 If another program has created the triangles, we probably do not know the grid that was used for Marching Cubes, or quite possibly no grid was used. In that case, we just save the vertex/triangle/value data in a compact form. For the we use an extension of the way edge points are encoded. We simply identify the minimum and maximum x, y, and z coordinates and then express the point as a fraction along each of those directions. Thus, the x, y, and z coordinate are within the interval [0,1]. We opt for the two-byte double-precision JVXL character compression. This allows a 1 part in 8100 resolution, which is plenty for these purposes. The tag will indicate the minimum and maximum values:- Parameters:
sb
-jvxlData
-vertexIdNew
-vertices
-vertexValues
-vertexCount
-polygonColorData
-polygonCount
-bsSlabDisplay
-vertexColors
-addColorData
-escapeXml
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jvxlFractionAsCharacter
public static char jvxlFractionAsCharacter(float fraction) -
jvxlFractionAsCharacterRange
public static char jvxlFractionAsCharacterRange(float fraction, int base, int range) -
jvxlAppendCharacter2
private static void jvxlAppendCharacter2(float value, float min, float max, int base, int range, javajs.util.SB list1, javajs.util.SB list2) -
jvxlFractionFromCharacter
public static float jvxlFractionFromCharacter(int ich, int base, int range, float fracOffset) -
jvxlFractionFromCharacter2
public static float jvxlFractionFromCharacter2(int ich1, int ich2, int base, int range) -
jvxlValueAsCharacter
public static char jvxlValueAsCharacter(float value, float min, float max, int base, int range) -
jvxlValueFromCharacter2
protected static float jvxlValueFromCharacter2(int ich, int ich2, float min, float max, int base, int range) -
jvxlEncodeBitSet0
public static int jvxlEncodeBitSet0(javajs.util.BS bs, int nPoints, javajs.util.SB sb) -
jvxlEncodeBitSet
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jvxlEncodeBitSetBuffer
public static int jvxlEncodeBitSetBuffer(javajs.util.BS bs, int nPoints, javajs.util.SB sb) -
jvxlAppendEncodedNumber
public static void jvxlAppendEncodedNumber(javajs.util.SB sb, int n, int base, int range) -
jvxlDecodeBitSetRange
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jvxlParseEncodedInt
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jvxlDecodeBitSet
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jvxlCompressString
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jvxlDecompressString
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jvxlCreateHeaderWithoutTitleOrAtoms
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jvxlCreateHeader
Creates a two-line header for the XJVXL file. It is no longer necessary to create the atom set or generate the vectors here. Please leave the commented code for posterity.- Parameters:
v
-sb
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