Revision: 5191
Author: hansonr
Date: 2006-05-28 22:35:14 -0700 (Sun, 28 May 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5191&view=rev
Log Message:
-----------
bob200603 stronger isosurface interpolation; some extra testing stuff
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
branches/bob200603/Jmol/src/org/jmol/viewer/Mesh.java
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-05-28
15:55:49 UTC (rev 5190)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-05-29
05:35:14 UTC (rev 5191)
@@ -188,7 +188,7 @@
currentMesh.visible = true;
discardTempData();
System.out.println("\n"
- + getJvxlFile(currentMesh, (iHaveColorData ? "mapped" : "")));
+ + getJvxlFile(currentMesh, (isJvxlColorMapped ? "mapped" : "")));
return;
}
if ("plane" == propertyName) {
@@ -247,8 +247,6 @@
}
boolean isJvxl;
- int[][] edgeInfo;
- int edgeCount;
void readData(boolean isMapData) {
isJvxl = false;
@@ -256,8 +254,8 @@
if (!isMapData) {
currentMesh.surfaceData = "";
currentMesh.edgeData = "";
- edgeInfo = null;
- edgeCount = 0;
+ currentMesh.edgeInfo = null;
+ currentMesh.edgeCount = 0;
}
int nSurfaces = readVolumetricHeader();
@@ -442,7 +440,7 @@
surfaceData = "";
strFractionTemp = "";
fractionData = "";
- iHaveColorData = false;
+ isJvxlColorMapped = false;
thisInside = (!isJvxl || thePlane == null);
nDataPoints = 0;
int nPointsX = voxelCounts[0];
@@ -499,7 +497,7 @@
currentMesh.jvxlPlane = thePlane;
}
System.out.println("Successfully read " + nPointsX + " x " + nPointsY
- + " x " + nPointsZ + " data points; " + edgeCount + " edges");
+ + " x " + nPointsZ + " data points; " + currentMesh.edgeCount + "
edges");
}
float calcVoxelPlaneDistance(int x, int y, int z) {
@@ -518,7 +516,7 @@
int nStructureData;
int nEdgeData;
int nColorData;
- boolean iHaveColorData;
+ boolean isJvxlColorMapped;
float jvxlCutoff;
void readJvxlDefinitionLine(boolean showMsg) throws Exception {
@@ -543,7 +541,7 @@
}
System.out.println("plane read: " + thePlane);
}
- iHaveColorData = (nColorData > 0);
+ isJvxlColorMapped = (nColorData > 0);
}
int thisValue;
@@ -607,12 +605,12 @@
if (isJvxl) {
readJvxlDefinitionLine(true);
System.out.println("JVXL skipping: nStructureData=" + nStructureData
- + " nEdgeData=" + nEdgeData + " iHaveColorData=" + iHaveColorData);
+ + " nEdgeData=" + nEdgeData + " isJvxlColorMapped=" +
isJvxlColorMapped);
if (nStructureData > 0)
skipData(nPoints, true);
if (nEdgeData > 0)
skipData(nEdgeData, false);
- if (iHaveColorData)
+ if (isJvxlColorMapped)
skipData(nColorData, false);
} else {
skipData(nPoints, true);
@@ -726,7 +724,7 @@
+ insideCount + " outsideCount=" + outsideCount + " surfaceCount="
+ surfaceCount + " total="
+ (insideCount + outsideCount + surfaceCount));
- if (iHaveColorData) {
+ if (isJvxlColorMapped) {
fractionPtr = 0;
setJvxlColixes(currentMesh, "roygb");
currentMesh.colorData = fractionData;
@@ -810,9 +808,10 @@
float valueA = vertexValues[vertexA];
float valueB = vertexValues[vertexB];
calcVertexPoints(vertexA, vertexB);
- addEdgeInfo(x, y, z, vertexA, vertexB);
float fraction = calcSurfacePoint(cutoff, valueA, valueB,
surfacePoints[iEdge]);
+ //currentMesh.addEdgeInfo(x, y, z, cubeVertexOffsets[vertexA],
+ // cubeVertexOffsets[vertexB], edgeTypeTable[iEdge], fraction);
int assocVertex = (fraction < assocCutoff ? -1
: fraction > 1 - assocCutoff ? 1 : 0);
String sKey = (assocVertex == 0 ? "" : calcDataKey(x, y, z,
@@ -948,21 +947,6 @@
voxelOrigin.scaleAdd(z, volumetricVectors[2], voxelOrigin);
}
- void addEdgeInfo(int x, int y, int z, int vertexA, int vertexB) {
- if (edgeInfo == null)
- edgeInfo = new int[256][];
- else if (edgeCount == edgeInfo.length)
- edgeInfo = (int[][]) Util.doubleLength(edgeInfo);
- int i = edgeCount++;
- edgeInfo[i] = new int[6];
- edgeInfo[i][0] = x + cubeVertexOffsets[vertexA].x;
- edgeInfo[i][1] = y + cubeVertexOffsets[vertexA].y;
- edgeInfo[i][2] = z + cubeVertexOffsets[vertexA].z;
- edgeInfo[i][3] = x + cubeVertexOffsets[vertexB].x;
- edgeInfo[i][4] = y + cubeVertexOffsets[vertexB].y;
- edgeInfo[i][5] = z + cubeVertexOffsets[vertexB].z;
- }
-
final static Point3i[] cubeVertexOffsets = { new Point3i(0, 0, 0),
new Point3i(1, 0, 0), new Point3i(1, 0, 1), new Point3i(0, 0, 1),
new Point3i(0, 1, 0), new Point3i(1, 1, 0), new Point3i(1, 1, 1),
@@ -991,6 +975,35 @@
return v;
}
+ /* Y
+ * 4 --------4--------- 5
+ * /| /|
+ * / | / |
+ * / | / |
+ * 7 8 5 |
+ * / | / 9
+ * / | / |
+ * 7 --------6--------- 6 |
+ * | | | |
+ * | 0 ---------0--|----- 1 X
+ * | / | /
+ * 11 / 10 /
+ * | 3 | 1
+ * | / | /
+ * | / | /
+ * 3 ---------2-------- 2
+ * Z
+ *
+ *
+ * type 0: x-edges: 0 2 4 6
+ * typw 1: y-edges: 8 9 10 11
+ * type 2: z-edges: 1 3 5 7
+ *
+ *
+ *
+ */
+ final static int edgeTypeTable[] = { 0, 2, 0, 2, 0, 2, 0, 2, 1, 1, 1, 1};
+
final static byte edgeVertexes[] = { 0, 1, 1, 2, 2, 3, 3, 0, 4, 5, 5, 6, 6,
7, 7, 4, 0, 4, 1, 5, 2, 6, 3, 7 };
@@ -1407,8 +1420,14 @@
mesh.vertexColixes = colixes = new short[vertexCount];
float diff = max - min;
String list = "";
- for (int i = 0; i < vertexCount; i++) {
+ //int edgePtr = 0;
+ int incr = (mesh.hasGridPoints ? 3 : 1);
+ for (int i = 0; i < vertexCount; i += incr) {
float value = lookupInterpolatedVoxelValue(vertexes[i]);
+ //assumes two volume sets are identical:
+ //float value = lookupInterpolatedVoxelValue(vertexes[i],
mesh.edgeInfo[edgePtr], mesh.fractionInfo[edgePtr]);
+ //float value = lookupInterpolatedVoxelValue(vertexes[i],
mesh.edgeInfo[edgePtr], (int)mesh.edgeData.charAt(edgePtr));
+ //++edgePtr;
if (value < min) {
value = min + diff * 0.0001f;
}
@@ -1429,8 +1448,14 @@
int vertexCount = mesh.vertexCount;
Point3f[] vertexes = mesh.vertices;
float min = Float.MAX_VALUE;
- for (int i = vertexCount; --i >= 0;) {
+ //int edgePtr = 0;
+ int incr = (mesh.hasGridPoints ? 3 : 1);
+ for (int i = 0; i < vertexCount; i += incr) {
float challenger = lookupInterpolatedVoxelValue(vertexes[i]);
+ //assumes two volume sets are identical:
+ //float challenger = lookupInterpolatedVoxelValue(vertexes[i],
mesh.edgeInfo[edgePtr], mesh.fractionInfo[edgePtr]);
+ //float challenger = lookupInterpolatedVoxelValue(vertexes[i],
mesh.edgeInfo[edgePtr], (int)mesh.edgeData.charAt(edgePtr));
+ //++edgePtr;
if (challenger < min)
min = challenger;
}
@@ -1441,18 +1466,40 @@
int vertexCount = mesh.vertexCount;
Point3f[] vertexes = mesh.vertices;
float max = -Float.MAX_VALUE;
- for (int i = vertexCount; --i >= 0;) {
+ //int edgePtr = 0;
+ int incr = (mesh.hasGridPoints ? 3 : 1);
+ for (int i = 0; i < vertexCount; i += incr) {
float challenger = lookupInterpolatedVoxelValue(vertexes[i]);
+ //float challenger = lookupInterpolatedVoxelValue(vertexes[i],
mesh.edgeInfo[edgePtr], mesh.fractionInfo[edgePtr]);
+ //float challenger = lookupInterpolatedVoxelValue(vertexes[i],
mesh.edgeInfo[edgePtr], (int)mesh.edgeData.charAt(edgePtr));
+ //++edgePtr;
if (challenger > max)
max = challenger;
}
return max;
}
- int i;
+
+ //approximation based on 90-cell bins
+ float lookupInterpolatedVoxelValue(Point3f point, int[]edgeXYZ, int ich) {
+ float fraction = fractionFromCharacter(ich, edgeFractionBase,
edgeFractionRange, 0.5f);
+ float valueA = voxelData[edgeXYZ[0]][edgeXYZ[1]][edgeXYZ[2]];
+ float valueB = voxelData[edgeXYZ[3]][edgeXYZ[4]][edgeXYZ[5]];
+ return valueA + fraction * (valueB - valueA);
+ }
+
+ //perfect interpolation -- volume blocks identical
+ float lookupInterpolatedVoxelValue(Point3f point, int[]edgeXYZ, float
fraction) {
+ float valueA = voxelData[edgeXYZ[0]][edgeXYZ[1]][edgeXYZ[2]];
+ float valueB = voxelData[edgeXYZ[3]][edgeXYZ[4]][edgeXYZ[5]];
+ return valueA + fraction * (valueB - valueA);
+ }
+
final Vector3f pointVector = new Vector3f();
final Point3f cubeLocation = new Point3f();
+ //generic for nonequivalent volume sets
+
float lookupInterpolatedVoxelValue(Point3f point) {
pointVector.sub(point, volumetricOrigin);
float x = scaleByVoxelVector(pointVector, 0);
@@ -1465,63 +1512,41 @@
return (vector.dot(unitVolumetricVectors[voxelVectorIndex]) /
volumetricVectorLengths[voxelVectorIndex]);
}
- int indexDown(float value, int voxelVectorIndex) {
+ int indexDown(float value, int iMax) {
+ if (value < 0)
+ return 0;
int floor = (int) value;
- float delta = value - floor;
- if (delta > 0.9f)
- ++floor;
- int lastValue = voxelCounts[voxelVectorIndex] - 1;
- if (floor > lastValue)
- floor = lastValue;
- return floor;
+ return (floor >= iMax ? iMax - 1 : floor);
}
- int indexUp(float value, int voxelVectorIndex) {
+ int indexUp(float value, int iMax) {
if (value < 0)
return 0;
int ceil = ((int) value) + 1;
- float delta = ceil - value;
- if (delta > 0.9f)
- --ceil;
- int lastValue = voxelCounts[voxelVectorIndex] - 1;
- if (ceil > lastValue)
- ceil = lastValue;
- return ceil;
+ return (ceil >= iMax ? iMax - 1 : ceil);
}
float getInterpolatedValue(float x, float y, float z) {
- int xDown = indexDown(x, 0);
- int xUp = indexUp(x, 0);
- int yDown = indexDown(y, 1);
- int yUp = indexUp(y, 1);
- int zDown = indexDown(z, 2);
- int zUp = indexUp(z, 2);
+ int iMax;
+ int xDown = indexDown(x, iMax = voxelCounts[0]);
+ int xUp = indexUp(x, iMax);
+ int yDown = indexDown(y, iMax = voxelCounts[1]);
+ int yUp = indexUp(y, iMax);
+ int zDown = indexDown(z, iMax = voxelCounts[2]);
+ int zUp = indexUp(z, iMax);
- float valueDown = voxelData[xDown][yDown][zDown];
- float valueUp = voxelData[xUp][yUp][zUp];
- float valueDelta = valueUp - valueDown;
- float delta;
- int differentMask;
- differentMask = ((((xUp == xDown) ? 0 : 1) << 0)
- | (((yUp == yDown) ? 0 : 1) << 1) | (((zUp == zDown) ? 0 : 1) << 2));
- switch (differentMask) {
- case 0:
- return valueDown;
- case 1:
- delta = x - xDown;
- break;
- case 2:
- delta = y - yDown;
- break;
- case 4:
- delta = z - zDown;
- break;
- default:
- // I don't feel like dealing with all the cases
- // just stick it in the middle
- delta = 0.5f;
- }
- return valueDown + delta * valueDelta;
-
+ float v1 = getFractional2DValue(x - xDown, y - yDown,
+ voxelData[xDown][yDown][zDown], voxelData[xUp][yDown][zDown],
+ voxelData[xDown][yUp][zDown], voxelData[xUp][yUp][zDown]);
+ float v2 = getFractional2DValue(x - xDown, y - yDown,
+ voxelData[xDown][yDown][zUp], voxelData[xUp][yDown][zUp],
+ voxelData[xDown][yUp][zUp], voxelData[xUp][yUp][zUp]);
+ return v1 + (z - zDown) * (v2 - v1);
}
+
+ float getFractional2DValue(float fx, float fy, float x11, float x12, float
x21, float x22) {
+ float v1 = x11 + fx * (x12 - x11);
+ float v2 = x21 + fx * (x22 - x21);
+ return v1 + fy * (v2 - v1);
+ }
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Mesh.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Mesh.java 2006-05-28
15:55:49 UTC (rev 5190)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Mesh.java 2006-05-29
05:35:14 UTC (rev 5191)
@@ -27,6 +27,7 @@
import org.jmol.g3d.*;
+import javax.vecmath.Point3i;
import javax.vecmath.Point3f;
import javax.vecmath.Point4f;
import javax.vecmath.Vector3f;
@@ -44,6 +45,9 @@
int nBytes;
boolean hasGridPoints;
boolean hideBackground;
+ int[][] edgeInfo;
+ float[] fractionInfo;
+ int edgeCount;
boolean visible = true;
short colix;
@@ -414,4 +418,24 @@
}
}
+ void addEdgeInfo(int x, int y, int z, Point3i offsetA, Point3i offsetB, int
edgeType, float fraction) {
+ // not used currently
+ if (edgeInfo == null) {
+ edgeInfo = new int[256][];
+ fractionInfo = new float[256];
+ } else if (edgeCount == edgeInfo.length) {
+ edgeInfo = (int[][]) Util.doubleLength(edgeInfo);
+ fractionInfo = (float[]) Util.doubleLength(fractionInfo);
+ }
+ int i = edgeCount++;
+ edgeInfo[i] = new int[6];
+ edgeInfo[i][0] = x + offsetA.x;
+ edgeInfo[i][1] = y + offsetA.y;
+ edgeInfo[i][2] = z + offsetA.z;
+ edgeInfo[i][3] = x + offsetB.x;
+ edgeInfo[i][4] = y + offsetB.y;
+ edgeInfo[i][5] = z + offsetB.z;
+ fractionInfo[i] = fraction;
+ }
+
}
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