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[Jmol-commits] SF.net SVN: jmol:[10675] trunk/Jmol
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From: <ha...@us...> - 2009-02-24 03:08:33
|
Revision: 10675
http://jmol.svn.sourceforge.net/jmol/?rev=10675&view=rev
Author: hansonr
Date: 2009-02-24 03:08:26 +0000 (Tue, 24 Feb 2009)
Log Message:
-----------
version=11.7.27_dev polygonColixes[] support
# new feature: JVXL format supports polygonColixes[]
# code: polygonColixes[] to define polygon colors rather than vertex-based colors (as in OBJ file)
Modified Paths:
--------------
trunk/Jmol/applet.classes
trunk/Jmol/appletweb/Jmol.js
trunk/Jmol/src/org/jmol/api/JmolExportInterface.java
trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
trunk/Jmol/src/org/jmol/export/Export3D.java
trunk/Jmol/src/org/jmol/export/IsosurfaceGenerator.java
trunk/Jmol/src/org/jmol/export/LcaoCartoonGenerator.java
trunk/Jmol/src/org/jmol/export/MolecularOrbitalGenerator.java
trunk/Jmol/src/org/jmol/export/PmeshGenerator.java
trunk/Jmol/src/org/jmol/export/_MayaExporter.java
trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
trunk/Jmol/src/org/jmol/export/_U3dExporter.java
trunk/Jmol/src/org/jmol/export/_VrmlExporter.java
trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
trunk/Jmol/src/org/jmol/jvxl/api/MeshDataServer.java
trunk/Jmol/src/org/jmol/jvxl/api/VertexDataServer.java
trunk/Jmol/src/org/jmol/jvxl/calc/MarchingCubes.java
trunk/Jmol/src/org/jmol/jvxl/calc/MarchingSquares.java
trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java
trunk/Jmol/src/org/jmol/jvxl/readers/EfvetReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/ObjReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
trunk/Jmol/src/org/jmol/shape/MeshRenderer.java
trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/applet.classes
===================================================================
--- trunk/Jmol/applet.classes 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/applet.classes 2009-02-24 03:08:26 UTC (rev 10675)
@@ -17,6 +17,9 @@
org/jmol/geodesic/*.java
org/jmol/i18n/*.java
+org/jmol/jvxl/data/*.java
+org/jmol/jvxl/calc/*.java
+org/jmol/jvxl/readers/*.java
org/jmol/jvxl/*.java
org/jmol/minimize/*.java
Modified: trunk/Jmol/appletweb/Jmol.js
===================================================================
--- trunk/Jmol/appletweb/Jmol.js 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/appletweb/Jmol.js 2009-02-24 03:08:26 UTC (rev 10675)
@@ -97,6 +97,9 @@
////////////////////////////////////////////////////////////////
function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
+ if (_jmol.initialized)
+ return;
+ _jmol.initialized = true;
if(allowJMOLJAR && document.location.search.indexOf("JMOLJAR=")>=0) {
var f = document.location.search.split("JMOLJAR=")[1].split("&")[0];
if (f.indexOf("/") >= 0) {
@@ -116,7 +119,6 @@
_jmolSetCodebase(codebaseDirectory);
_jmolGetJarFilename(fileNameOrUseSignedApplet);
_jmolOnloadResetForms();
- _jmol.initialized = true;
}
function jmolSetTranslation(TF) {
@@ -729,11 +731,11 @@
}
if (useIEObject) { // use MSFT IE6 object tag with .cab file reference
winCodebase = (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "");
+ params.code = 'JmolApplet';
tHeader =
"<object name='jmolApplet" + nameSuffix +
"' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
" classid='" + windowsClassId + "'\n" + winCodebase + widthAndHeight + ">\n";
- params.code = 'JmolApplet';
tFooter = "</object>";
} else if (useHtml4Object) { // use HTML4 object tag
tHeader =
@@ -797,8 +799,6 @@
if (_jmol.initChecked)
return;
_jmol.initChecked = true;
- if (_jmol.initialized)
- return;
jmolInitialize(defaultdir, defaultjar)
}
@@ -1087,6 +1087,7 @@
}
function _jmolOnloadResetForms() {
+ // must be evaluated ONLY once
_jmol.previousOnloadHandler = window.onload;
window.onload =
function() {
Modified: trunk/Jmol/src/org/jmol/api/JmolExportInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolExportInterface.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/api/JmolExportInterface.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -42,7 +42,8 @@
abstract void renderIsosurface(Point3f[] vertices, short colix,
short[] colixes, Vector3f[] normals,
int[][] indices, BitSet bsFaces,
- int nVertices, int faceVertexMax);
+ int nVertices, int faceVertexMax,
+ short[] polygonColixes, int nPolygons);
abstract void renderText(Text t);
Modified: trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/api/JmolRendererInterface.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -287,7 +287,7 @@
public abstract void renderIsosurface(Point3f[] vertices, short colix,
short[] colixes, Vector3f[] normals,
int[][] indices, BitSet bsFaces, int nVertices,
- int faceVertexMax);
+ int faceVertexMax, short[] polygonColixes, int nPolygons);
public abstract boolean isInDisplayRange(int x, int y);
Modified: trunk/Jmol/src/org/jmol/export/Export3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/Export3D.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/export/Export3D.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -652,9 +652,9 @@
public void renderIsosurface(Point3f[] vertices, short colix,
short[] colixes, Vector3f[] normals,
int[][] indices, BitSet bsFaces, int nVertices,
- int faceVertexMax) {
+ int faceVertexMax, short[] polygonColixes, int nPolygons) {
exporter.renderIsosurface(vertices, colix, colixes, normals,
- indices, bsFaces, nVertices, faceVertexMax);
+ indices, bsFaces, nVertices, faceVertexMax, null, nPolygons);
}
public void renderEllipsoid(int x, int y, int z, int diameter,
Modified: trunk/Jmol/src/org/jmol/export/IsosurfaceGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/IsosurfaceGenerator.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/export/IsosurfaceGenerator.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -32,6 +32,7 @@
protected void renderExport() {
g3d.getExporter().renderIsosurface(imesh.vertices, imesh.colix,
imesh.isColorSolid ? null : imesh.vertexColixes,
- imesh.getVertexNormals(), imesh.polygonIndexes, bsFaces, imesh.vertexCount, 3);
+ imesh.getVertexNormals(), imesh.polygonIndexes, bsFaces, imesh.vertexCount, 3,
+ imesh.isColorSolid ? imesh.polygonColixes : null, imesh.polygonCount);
}
}
Modified: trunk/Jmol/src/org/jmol/export/LcaoCartoonGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/LcaoCartoonGenerator.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/export/LcaoCartoonGenerator.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -32,6 +32,7 @@
protected void renderExport() {
g3d.getExporter().renderIsosurface(imesh.vertices, imesh.colix,
imesh.isColorSolid ? null : imesh.vertexColixes,
- imesh.getVertexNormals(), imesh.polygonIndexes, bsFaces, imesh.vertexCount, 3);
+ imesh.getVertexNormals(), imesh.polygonIndexes, bsFaces, imesh.vertexCount, 3,
+ imesh.polygonColixes, imesh.polygonCount);
}
}
Modified: trunk/Jmol/src/org/jmol/export/MolecularOrbitalGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/MolecularOrbitalGenerator.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/export/MolecularOrbitalGenerator.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -32,6 +32,7 @@
protected void renderExport() {
g3d.getExporter().renderIsosurface(imesh.vertices, imesh.colix,
imesh.isColorSolid ? null : imesh.vertexColixes,
- imesh.getVertexNormals(), imesh.polygonIndexes, bsFaces, imesh.vertexCount, 3);
+ imesh.getVertexNormals(), imesh.polygonIndexes, bsFaces,
+ imesh.vertexCount, 3, null, imesh.polygonCount);
}
}
Modified: trunk/Jmol/src/org/jmol/export/PmeshGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/PmeshGenerator.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/export/PmeshGenerator.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -31,7 +31,7 @@
protected void renderExport() {
g3d.getExporter().renderIsosurface(mesh.vertices, mesh.colix, null,
- mesh.getVertexNormals(), mesh.polygonIndexes, bsFaces, mesh.vertexCount,
- 4);
+ mesh.getVertexNormals(), mesh.polygonIndexes, bsFaces,
+ mesh.vertexCount, 4, null, mesh.polygonCount);
}
}
Modified: trunk/Jmol/src/org/jmol/export/_MayaExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_MayaExporter.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/export/_MayaExporter.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -157,7 +157,8 @@
public void renderIsosurface(Point3f[] vertices, short colix,
short[] colixes, Vector3f[] normals,
int[][] indices, BitSet bsFaces,
- int nVertices, int faceVertexMax) {
+ int nVertices, int faceVertexMax,
+ short[] polygonColixes, int nPolygons) {
}
public void renderText(Text t) {
Modified: trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -40,7 +40,6 @@
import org.jmol.g3d.Graphics3D;
import org.jmol.modelset.Atom;
import org.jmol.shape.Text;
-import org.jmol.util.BitSetUtil;
import org.jmol.util.TextFormat;
import org.jmol.viewer.JmolConstants;
import org.jmol.viewer.Viewer;
@@ -406,20 +405,43 @@
public void renderIsosurface(Point3f[] vertices, short colix,
short[] colixes, Vector3f[] normals,
int[][] indices, BitSet bsFaces, int nVertices,
- int faceVertexMax) {
+ int faceVertexMax, short[] polygonColixes, int nPolygons) {
if (nVertices == 0)
return;
int nFaces = 0;
- for (int i = BitSetUtil.length(bsFaces); --i >= 0;)
+ for (int i = nPolygons; --i >= 0;)
if (bsFaces.get(i))
nFaces += (faceVertexMax == 4 && indices[i].length == 4 ? 2 : 1);
if (nFaces == 0)
return;
+
+ if (polygonColixes != null) {
+ for (int i = nPolygons; --i >= 0;) {
+ if (!bsFaces.get(i))
+ continue;
+ //if ((p++) % 10 == 0)
+ // output("\n");
+ output("polygon { 4\n");
+ for (int j = 0; j <= 3; j++) {
+ viewer.transformPoint(vertices[indices[i][j % 3]], tempP1);
+ output(", <" + triad(tempP1) + ">");
+ }
+ output("\n");
+ output("pigment{rgbt<" + color4(colix = polygonColixes[i]) + ">}\n");
+ output(" translucentFinish(" + translucencyFractionalFromColix(colix)
+ + ")\n");
+ output(" check_shadow()\n");
+ output(" clip()\n");
+ output("}\n");
+ }
+
+ return;
+ }
+
Hashtable htColixes = new Hashtable();
String color;
output("mesh2 {\n");
-
output("vertex_vectors { " + nVertices);
for (int i = 0; i < nVertices; i++) {
//if (i % 10 == 0)
@@ -467,7 +489,7 @@
}
output("face_indices { " + nFaces);
//int p = 0;
- for (int i = BitSetUtil.length(bsFaces); --i >= 0;) {
+ for (int i = nPolygons; --i >= 0;) {
if (!bsFaces.get(i))
continue;
//if ((p++) % 10 == 0)
Modified: trunk/Jmol/src/org/jmol/export/_U3dExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_U3dExporter.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/export/_U3dExporter.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -35,7 +35,6 @@
import org.jmol.g3d.Font3D;
import org.jmol.modelset.Atom;
import org.jmol.shape.Text;
-import org.jmol.util.BitSetUtil;
public class _U3dExporter extends _Exporter {
@@ -121,16 +120,17 @@
public void renderIsosurface(Point3f[] vertices, short colix,
short[] colixes, Vector3f[] normals,
int[][] indices, BitSet bsFaces, int nVertices,
- int faceVertexMax) {
+ int faceVertexMax, short[] polygonColixes, int nPolygons) {
if (nVertices == 0)
return;
int nFaces = 0;
- for (int i = BitSetUtil.length(bsFaces); --i >= 0;)
+ for (int i = nPolygons; --i >= 0;)
if (bsFaces.get(i))
nFaces += (faceVertexMax == 4 && indices[i].length == 4 ? 2 : 1);
if (nFaces == 0)
return;
+ //TODO
/*
String color = rgbFractionalFromColix(colix, ' ');
output("Shape {\n");
Modified: trunk/Jmol/src/org/jmol/export/_VrmlExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_VrmlExporter.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/export/_VrmlExporter.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -35,7 +35,6 @@
import org.jmol.g3d.Font3D;
import org.jmol.modelset.Atom;
import org.jmol.shape.Text;
-import org.jmol.util.BitSetUtil;
import org.jmol.viewer.Viewer;
@@ -146,12 +145,12 @@
public void renderIsosurface(Point3f[] vertices, short colix,
short[] colixes, Vector3f[] normals,
int[][] indices, BitSet bsFaces, int nVertices,
- int faceVertexMax) {
+ int faceVertexMax, short[] polygonColixes, int nPolygons) {
if (nVertices == 0)
return;
int nFaces = 0;
- for (int i = BitSetUtil.length(bsFaces); --i >= 0;)
+ for (int i = nPolygons; --i >= 0;)
if (bsFaces.get(i))
nFaces += (faceVertexMax == 4 && indices[i].length == 4 ? 2 : 1);
if (nFaces == 0)
@@ -178,7 +177,7 @@
output(" }\n");
output(" coordIndex [\n");
String sep = " ";
- for (int i = BitSetUtil.length(bsFaces); --i >= 0;) {
+ for (int i = nPolygons; --i >= 0;) {
if (!bsFaces.get(i))
continue;
output(sep + indices[i][0] + " " + indices[i][1] + " " + indices[i][2]
Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -1463,7 +1463,7 @@
public void renderIsosurface(Point3f[] vertices, short colix,
short[] colixes, Vector3f[] normals,
int[][] indices, BitSet bsFaces, int nVertices,
- int faceVertexMax) {
+ int faceVertexMax, short[] polygonColixes, int nPolygons) {
// generator only
}
Modified: trunk/Jmol/src/org/jmol/jvxl/api/MeshDataServer.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/api/MeshDataServer.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/api/MeshDataServer.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -32,4 +32,5 @@
public abstract void notifySurfaceGenerationCompleted();
public abstract void notifySurfaceMappingCompleted();
public abstract Point3f[] calculateGeodesicSurface(BitSet bsSelected, float envelopeRadius);
+ public abstract int getColixArgb(short colix);
}
Modified: trunk/Jmol/src/org/jmol/jvxl/api/VertexDataServer.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/api/VertexDataServer.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/api/VertexDataServer.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -95,9 +95,10 @@
* @param iC
* @param check
* @param isAbsolute
+ * @param color
*/
public abstract void addTriangleCheck(int iA, int iB, int iC, int check,
- boolean isAbsolute);
+ boolean isAbsolute, int color);
/**
*
Modified: trunk/Jmol/src/org/jmol/jvxl/calc/MarchingCubes.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/calc/MarchingCubes.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/calc/MarchingCubes.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -305,7 +305,7 @@
surfaceReader.addTriangleCheck(edgePointIndexes[ia],
edgePointIndexes[ib], edgePointIndexes[ic],
- edgeType, isCutoffAbsolute);
+ edgeType, isCutoffAbsolute, 0);
}
Modified: trunk/Jmol/src/org/jmol/jvxl/calc/MarchingSquares.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/calc/MarchingSquares.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/calc/MarchingSquares.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -966,7 +966,7 @@
: iA == mesh1 && iC == mesh2 || iC == mesh1 && iA == mesh2 ? 4
: 0);
if (iA >= 0 && iB >= 0 && iC >= 0)
- surfaceReader.addTriangleCheck(iA, iB, iC, check, false);
+ surfaceReader.addTriangleCheck(iA, iB, iC, check, false, 0);
k = triangleVertexList[i];
}
}
Modified: trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/data/MeshData.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -117,6 +117,7 @@
import javax.vecmath.Point3f;
+import org.jmol.g3d.Graphics3D;
import org.jmol.util.*;
public class MeshData {
@@ -133,6 +134,7 @@
public int vertexCount;
public float[] vertexValues;
public int[][] polygonIndexes;
+ public short[] polygonColixes;
public BitSet[] surfaceSet;
public int[] vertexSets;
@@ -172,7 +174,10 @@
return vertexCount++;
}
- public void addTriangleCheck(int vertexA, int vertexB, int vertexC, int check) {
+ private int lastColor;
+ private short lastColix;
+
+ public void addTriangleCheck(int vertexA, int vertexB, int vertexC, int check, int color) {
if (vertexValues != null && (Float.isNaN(vertexValues[vertexA])||Float.isNaN(vertexValues[vertexB])||Float.isNaN(vertexValues[vertexC])))
return;
if (Float.isNaN(vertices[vertexA].x)||Float.isNaN(vertices[vertexB].x)||Float.isNaN(vertices[vertexC].x))
@@ -181,6 +186,16 @@
polygonIndexes = new int[SEED_COUNT][];
else if (polygonCount == polygonIndexes.length)
polygonIndexes = (int[][]) ArrayUtil.doubleLength(polygonIndexes);
+ if (color != 0) {
+ if (polygonColixes == null) {
+ polygonColixes = new short[SEED_COUNT];
+ lastColor = 0;
+ }
+ else if (polygonCount == polygonColixes.length) {
+ polygonColixes = (short[]) ArrayUtil.doubleLength(polygonColixes);
+ }
+ polygonColixes[polygonCount] = (color == lastColor ? lastColix : (lastColix = Graphics3D.getColix(lastColor = color)));
+ }
polygonIndexes[polygonCount++] = new int[] {vertexA, vertexB, vertexC, check};
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/EfvetReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/EfvetReader.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/EfvetReader.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -126,7 +126,7 @@
nTriangles = parseInt();
for (int i = 0; i < nTriangles; i++) {
skipTo("<triangle", "vertex");
- addTriangleCheck(parseInt() - 1, parseInt() - 1, parseInt() - 1, 7, false);
+ addTriangleCheck(parseInt() - 1, parseInt() - 1, parseInt() - 1, 7, false, 0);
}
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -32,6 +32,7 @@
import org.jmol.shapesurface.IsosurfaceMesh;
import org.jmol.util.*;
+import org.jmol.jvxl.api.MeshDataServer;
import org.jmol.jvxl.data.JvxlData;
import org.jmol.jvxl.data.MeshData;
import org.jmol.jvxl.data.VolumeData;
@@ -915,7 +916,8 @@
//0.9e adds color contours for planes and min/max range, contour settings
}
- public static String jvxlGetFile(JvxlData jvxlData, MeshData meshData,
+ public static String jvxlGetFile(MeshDataServer meshDataServer,
+ JvxlData jvxlData, MeshData meshData,
String[] title, String msg,
boolean includeHeader, int nSurfaces,
String state, String comment) {
@@ -942,16 +944,16 @@
sb.append("<jvxlSurfaceData>\n");
sb.append(jvxlEncodeTriangleData(meshData.polygonIndexes,
meshData.polygonCount, vertexIdNew));
- sb.append(jvxlEncodeVertexData(jvxlData, vertexIdNew, meshData.vertices,
- meshData.vertexValues, meshData.vertexCount, jvxlData.jvxlColorData
- .length() > 0));
+ sb.append(jvxlEncodeVertexData(meshDataServer, jvxlData, vertexIdNew,
+ meshData.vertices, meshData.vertexValues, meshData.vertexCount,
+ meshData.polygonColixes, meshData.polygonCount,
+ jvxlData.jvxlColorData.length() > 0));
sb.append("</jvxlSurfaceData>\n");
} else if (jvxlData.jvxlPlane == null) {
//no real point in compressing this unless it's a sign-based coloring
sb.append(jvxlData.jvxlSurfaceData);
- sb.append(jvxlCompressString(jvxlData.jvxlEdgeData))
- .append('\n').append(jvxlCompressString(jvxlData.jvxlColorData))
- .append('\n');
+ sb.append(jvxlCompressString(jvxlData.jvxlEdgeData)).append('\n').append(
+ jvxlCompressString(jvxlData.jvxlColorData)).append('\n');
} else {
sb.append(jvxlCompressString(jvxlData.jvxlColorData)).append('\n');
}
@@ -975,13 +977,14 @@
data.append("</jvxlContourData>\n");
}
if (comment != null)
- data.append("<jvxlSurfaceCommand>\n ").append(comment).append(
- "\n</jvxlSurfaceCommand>\n");
+ data.append("<jvxlSurfaceCommand>\n ").append(comment).append(
+ "\n</jvxlSurfaceCommand>\n");
if (state != null)
- data.append("<jvxlSurfaceState>\n ").append(state).append(
- "\n</jvxlSurfaceState>\n");
+ data.append("<jvxlSurfaceState>\n ").append(state).append(
+ "\n</jvxlSurfaceState>\n");
if (includeHeader)
- data.append("<jvxlFileTitle>\n").append(jvxlData.jvxlFileTitle).append("</jvxlFileTitle>\n");
+ data.append("<jvxlFileTitle>\n").append(jvxlData.jvxlFileTitle).append(
+ "</jvxlFileTitle>\n");
return data.toString();
}
@@ -1258,20 +1261,26 @@
* The resultant string is really two strings of length nData
* where the first string lists the "high" part of the positions,
* and the second string lists the "low" part of the positions.
+ * @param meshDataServer
*
* @param jvxlData
* @param vertexIdNew
* @param vertices
* @param vertexValues
* @param vertexCount
+ * @param polygonColixes
+ * @param polygonCount
* @param addColorData
* @return string of encoded data
*/
- public static String jvxlEncodeVertexData(JvxlData jvxlData,
+ public static String jvxlEncodeVertexData(MeshDataServer meshDataServer,
+ JvxlData jvxlData,
int[] vertexIdNew,
Point3f[] vertices,
float[] vertexValues,
int vertexCount,
+ short[] polygonColixes,
+ int polygonCount,
boolean addColorData) {
Point3f min = new Point3f(Float.MAX_VALUE, Float.MAX_VALUE, Float.MAX_VALUE);
Point3f max = new Point3f(Float.MIN_VALUE, Float.MIN_VALUE, Float.MIN_VALUE);
@@ -1313,6 +1322,27 @@
list.append(" <jvxlVertexData len=\"" + list1.length() + "\" count=\""
+ vertexCount + "\" min=\"" + min + "\" max=\"" + max + "\">\n ");
list.append(list1).append("\n </jvxlVertexData>\n");
+ if (polygonColixes != null) {
+ list1 = new StringBuffer();
+ int count = 0;
+ short colix = 0;
+ boolean done = false;
+ for (int i = 0; i < polygonCount || (done = true) == true; i++) {
+ if (done || polygonColixes[i] != colix) {
+ if (count != 0)
+ list1.append(" ").append(count).append(" ").append(
+ (colix == 0 ? 0 : meshDataServer.getColixArgb(colix)));
+ if (done)
+ break;
+ colix = polygonColixes[i];
+ count = 1;
+ } else {
+ count++;
+ }
+ }
+ list.append(" <jvxlPolygonColorData len=\"" + list1.length() + "\" count=\""
+ + polygonCount+ "\">\n ").append(list1).append("\n </jvxlPolygonColorData>\n");
+ }
if (!addColorData)
return list.toString();
@@ -1342,7 +1372,8 @@
private void getEncodedVertexData() throws Exception {
String data = getXmlData("jvxlSurfaceData", null, true);
jvxlDecodeVertexData(getXmlData("jvxlVertexData", data, true), false);
- jvxlDecodeTriangleData(getXmlData("jvxlTriangleData", data, true), false);
+ String polygonColorData = getXmlData("jvxlPolygonColorData", data, false);
+ jvxlDecodeTriangleData(getXmlData("jvxlTriangleData", data, true), polygonColorData, false);
Logger.info("Checking for vertex values");
jvxlColorDataRead = jvxlUncompressString(getXmlData("jvxlColorData", data, false));
jvxlDataIsColorMapped = (jvxlColorDataRead.length() > 0);
@@ -1527,11 +1558,15 @@
* as created with jvxlEncodeTriangleData (see above)
*
* @param data tag and contents
+ * @param colorData
* @param asArray or just addTriangleCheck
* @return int[][] if desired
*/
- int[][] jvxlDecodeTriangleData(String data, boolean asArray) {
+ int[][] jvxlDecodeTriangleData(String data, String colorData, boolean asArray) {
int[] next = new int[1];
+ int[] nextc = new int[1];
+ int nColors = (colorData == null ? -1 : 0);
+ int color = 0;
setNext(data, "count", next, 2);
int nData = Parser.parseInt(data, next);
if (!asArray)
@@ -1584,8 +1619,18 @@
if (++p % 3 == 0) {
i++;
p = 0;
- if (!asArray)
- addTriangleCheck(triangle[0], triangle[1], triangle[2], 7, false);
+ if (!asArray) {
+ if (nColors >= 0) {
+ if (nColors == 0) {
+ nColors = Parser.parseInt(colorData, nextc);
+ color = Parser.parseInt(colorData, nextc);
+ if (color == Integer.MIN_VALUE)
+ color = nColors = 0;
+ }
+ nColors--;
+ }
+ addTriangleCheck(triangle[0], triangle[1], triangle[2], 7, false, color);
+ }
}
}
return triangles;
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/ObjReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/ObjReader.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/ObjReader.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -27,6 +27,7 @@
import javax.vecmath.Point3f;
+import org.jmol.g3d.Graphics3D;
import org.jmol.util.Logger;
import org.jmol.util.Parser;
@@ -124,11 +125,15 @@
private boolean readPolygons() {
nPolygons = 0;
+ int color = 0;
try {
if (!params.readAllData) {
for (int i = 0; i < params.fileIndex; i++) {
while (line != null && line.indexOf("g ") != 0)
line = br.readLine();
+ if (line == null)
+ break;
+ color = Graphics3D.getArgbFromString("[" + line.substring(3) + "]");
line = br.readLine();
}
}
@@ -144,14 +149,16 @@
int vertexCount = (id == Integer.MIN_VALUE ? 3 : 4);
if (vertexCount == 4) {
nTriangles += 2;
- addTriangleCheck(ia - 1, ib - 1, ic - 1, 5, false);
- addTriangleCheck(ib - 1, ic - 1, id - 1, 3, false);
+ addTriangleCheck(ia - 1, ib - 1, ic - 1, 5, false, color);
+ addTriangleCheck(ib - 1, ic - 1, id - 1, 3, false, color);
} else {
nTriangles++;
- addTriangleCheck(ia - 1, ib - 1, ic - 1, 7, false);
+ addTriangleCheck(ia - 1, ib - 1, ic - 1, 7, false, color);
}
- } else if (line.indexOf("g ") == 0 && !params.readAllData) {
- break;
+ } else if (line.indexOf("g ") == 0) {
+ if (!params.readAllData)
+ break;
+ color = Graphics3D.getArgbFromString("[x" + line.substring(3) + "]");
}
line = br.readLine();
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -216,11 +216,11 @@
// 2
if (vertexCount == 4) {
nTriangles += 2;
- addTriangleCheck(vertices[0], vertices[1], vertices[3], 5, false);
- addTriangleCheck(vertices[1], vertices[2], vertices[3], 3, false);
+ addTriangleCheck(vertices[0], vertices[1], vertices[3], 5, false, 0);
+ addTriangleCheck(vertices[1], vertices[2], vertices[3], 3, false, 0);
} else {
nTriangles++;
- addTriangleCheck(vertices[0], vertices[1], vertices[2], 7, false);
+ addTriangleCheck(vertices[0], vertices[1], vertices[2], 7, false, 0);
}
}
return true;
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -911,7 +911,7 @@
public Object getProperty(String property, int index) {
if (property == "jvxlFileData")
- return JvxlReader.jvxlGetFile(jvxlData, null, params.title, "", true,
+ return JvxlReader.jvxlGetFile(meshDataServer, jvxlData, null, params.title, "", true,
index, null, null);
if (property == "jvxlFileInfo")
return jvxlData.jvxlInfoLine; // for Jvxl.java
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -508,14 +508,14 @@
}
public void addTriangleCheck(int iA, int iB, int iC, int check,
- boolean isAbsolute) {
+ boolean isAbsolute, int color) {
if (meshDataServer == null) {
if (isAbsolute
&& !MeshData.checkCutoff(iA, iB, iC, meshData.vertexValues))
return;
- meshData.addTriangleCheck(iA, iB, iC, check);
+ meshData.addTriangleCheck(iA, iB, iC, check, color);
} else {
- meshDataServer.addTriangleCheck(iA, iB, iC, check, isAbsolute);
+ meshDataServer.addTriangleCheck(iA, iB, iC, check, isAbsolute, color);
}
}
@@ -627,7 +627,7 @@
float[] vertexValues = meshData.vertexValues;
short[] vertexColixes = meshData.vertexColixes;
-
+ meshData.polygonColixes = null;
float valueBlue = jvxlData.valueMappedToBlue;
float valueRed = jvxlData.valueMappedToRed;
short minColorIndex = jvxlData.minColorIndex;
Modified: trunk/Jmol/src/org/jmol/shape/MeshRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/MeshRenderer.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/shape/MeshRenderer.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -231,7 +231,7 @@
protected void renderExport() {
//not implemented for this yet.
g3d.renderIsosurface(mesh.vertices, mesh.colix, null,
- mesh.getVertexNormals(), mesh.polygonIndexes, bsFaces, mesh.vertexCount, 4);
+ mesh.getVertexNormals(), mesh.polygonIndexes, bsFaces, mesh.vertexCount, 4, null, nPolygons);
}
}
Modified: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -202,10 +202,12 @@
if (thisMesh != null) {
//thisMesh.vertexColixes = null;
thisMesh.isColorSolid = true;
+ thisMesh.polygonColixes = null;
} else if (!TextFormat.isWild(previousMeshID)){
for (int i = meshCount; --i >= 0;) {
//isomeshes[i].vertexColixes = null;
isomeshes[i].isColorSolid = true;
+ isomeshes[i].polygonColixes = null;
}
}
setPropertySuper(propertyName, value, bs);
@@ -426,11 +428,11 @@
meshData = new MeshData();
fillMeshData(meshData, MeshData.MODE_GET_VERTICES);
}
- return JvxlReader.jvxlGetFile(jvxlData, meshData, title, "", true, index, thisMesh
+ return JvxlReader.jvxlGetFile(this, jvxlData, meshData, title, "", true, index, thisMesh
.getState(myType), (thisMesh.scriptCommand == null ? "" : thisMesh.scriptCommand));
}
if (property == "jvxlSurfaceData") // MO only
- return JvxlReader.jvxlGetFile(jvxlData, null, title, "", false, 1, thisMesh
+ return JvxlReader.jvxlGetFile(this, jvxlData, null, title, "", false, 1, thisMesh
.getState(myType), (thisMesh.scriptCommand == null ? "" : thisMesh.scriptCommand));
if (property == "jvxlFileInfo")
return jvxlData.jvxlInfoLine;
@@ -694,12 +696,14 @@
meshData.vertexIncrement = thisMesh.vertexIncrement;
meshData.polygonCount = thisMesh.polygonCount;
meshData.polygonIndexes = thisMesh.polygonIndexes;
+ meshData.polygonColixes = thisMesh.polygonColixes;
return;
case MeshData.MODE_GET_COLOR_INDEXES:
if (thisMesh.vertexColixes == null
|| thisMesh.vertexCount > thisMesh.vertexColixes.length)
thisMesh.vertexColixes = new short[thisMesh.vertexCount];
meshData.vertexColixes = thisMesh.vertexColixes;
+ meshData.polygonIndexes = null;
return;
case MeshData.MODE_PUT_SETS:
thisMesh.surfaceSet = meshData.surfaceSet;
@@ -714,6 +718,7 @@
thisMesh.vertexIncrement = meshData.vertexIncrement;
thisMesh.polygonCount = meshData.polygonCount;
thisMesh.polygonIndexes = meshData.polygonIndexes;
+ thisMesh.polygonColixes = meshData.polygonColixes;
return;
}
}
@@ -780,10 +785,10 @@
}
public void addTriangleCheck(int iA, int iB, int iC, int check,
- boolean isAbsolute) {
+ boolean isAbsolute, int color) {
if (isAbsolute && !MeshData.checkCutoff(iA, iB, iC, thisMesh.vertexValues))
return;
- thisMesh.addTriangleCheck(iA, iB, iC, check);
+ thisMesh.addTriangleCheck(iA, iB, iC, check, color);
}
////////////////////////////////////////////////////////////////////
@@ -851,6 +856,7 @@
JvxlData jvxlData = thisMesh.jvxlData;
float[] vertexValues = thisMesh.vertexValues;
short[] vertexColixes = thisMesh.vertexColixes;
+ thisMesh.polygonColixes = null;
if (vertexValues == null || jvxlData.isBicolorMap
|| jvxlData.vertexCount == 0)
return;
@@ -961,6 +967,9 @@
return (d2 < dmin2 ? d2 : -1);
}
+ public int getColixArgb(short colix) {
+ return viewer.getColixArgb(colix);
+ }
}
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -152,16 +152,37 @@
Graphics3D.getColixTranslucent(vertexColixes[i], isTranslucent, iLevel);
}
- void addTriangleCheck(int vertexA, int vertexB, int vertexC, int check) {
- if (vertices == null || vertexValues != null && (Float.isNaN(vertexValues[vertexA])||Float.isNaN(vertexValues[vertexB])||Float.isNaN(vertexValues[vertexC])))
+ public short[] polygonColixes;
+ private int lastColor;
+ private short lastColix;
+
+ void addTriangleCheck(int vertexA, int vertexB, int vertexC, int check,
+ int color) {
+ if (vertices == null
+ || vertexValues != null
+ && (Float.isNaN(vertexValues[vertexA])
+ || Float.isNaN(vertexValues[vertexB]) || Float
+ .isNaN(vertexValues[vertexC])))
return;
- if (Float.isNaN(vertices[vertexA].x)||Float.isNaN(vertices[vertexB].x)||Float.isNaN(vertices[vertexC].x))
+ if (Float.isNaN(vertices[vertexA].x) || Float.isNaN(vertices[vertexB].x)
+ || Float.isNaN(vertices[vertexC].x))
return;
if (polygonCount == 0)
polygonIndexes = new int[SEED_COUNT][];
else if (polygonCount == polygonIndexes.length)
polygonIndexes = (int[][]) ArrayUtil.doubleLength(polygonIndexes);
- polygonIndexes[polygonCount++] = new int[] {vertexA, vertexB, vertexC, check};
+ if (color != 0) {
+ if (polygonColixes == null) {
+ polygonColixes = new short[SEED_COUNT];
+ lastColor = 0;
+ } else if (polygonCount == polygonColixes.length) {
+ polygonColixes = (short[]) ArrayUtil.doubleLength(polygonColixes);
+ }
+ polygonColixes[polygonCount] = (color == lastColor ? lastColix
+ : (lastColix = Graphics3D.getColix(lastColor = color)));
+ }
+ polygonIndexes[polygonCount++] = new int[] { vertexA, vertexB, vertexC,
+ check };
}
void invalidateTriangles() {
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java 2009-02-24 03:08:26 UTC (rev 10675)
@@ -112,7 +112,7 @@
if (imesh.vertexColixes != null)
g3d.setColix(imesh.vertexColixes[i]);
g3d.fillSphereCentered(diam, screens[i]);
- if (showNumbers)
+ if (showNumbers && screens[i].z > 10)
g3d.drawStringNoSlab(i
+ (imesh.isColorSolid ? "" : " " + imesh.vertexValues[i]), null,
screens[i].x, screens[i].y, screens[i].z);
@@ -152,6 +152,7 @@
colorSolid = true;
colix = Graphics3D.BLACK;
}
+ boolean colorArrayed = (fill && colorSolid && imesh.polygonColixes != null);
// two-sided means like a plane, with no front/back distinction
for (int i = imesh.polygonCount; --i >= 0;) {
@@ -171,6 +172,11 @@
continue;
short colixA, colixB, colixC;
if (colorSolid) {
+ if (colorArrayed && i < imesh.polygonColixes.length) {
+ short c = imesh.polygonColixes[i];
+ if (c != 0)
+ colix = c;
+ }
colixA = colixB = colixC = colix;
} else {
colixA = vertexColixes[iA];
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-02-23 17:52:59 UTC (rev 10674)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-02-24 03:08:26 UTC (rev 10675)
@@ -3,6 +3,8 @@
version=11.7.27_dev
+# new feature: JVXL format supports polygonColixes[]
+# code: polygonColixes[] to define polygon colors rather than vertex-based colors (as in OBJ file)
# new feature: isosurface points can be retrieved using $id[n] where n=0,1,2,3... similar to $draw[n]
# debugging: setTestflag2() turns on vertex labeling in isosurfaces
# new feature: isosurface OBJ file reader using
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