Revision: 5169
Author: hansonr
Date: 2006-05-24 22:45:51 -0700 (Wed, 24 May 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5169&view=rev
Log Message:
-----------
bob200603 isosurfaces Phase III complete: planes
defined as Point4f in Eval: {a b c d} for ax + by + cz + d = 0.
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-05-25
03:47:48 UTC (rev 5168)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-05-25
05:45:51 UTC (rev 5169)
@@ -32,6 +32,7 @@
import java.util.Hashtable;
import javax.vecmath.Point3f;
import javax.vecmath.Vector3f;
+import javax.vecmath.Point4f;
class Context {
String filename;
@@ -1423,6 +1424,31 @@
return pt;
}
+ Point4f getPoint4f(int i) throws ScriptException {
+ coordinatesAreFractional = false;
+ if (statement[i++].tok != Token.leftbrace)
+ coordinateExpected();
+ Point4f pt = new Point4f();
+ for (int j = i; j + 1 < statement.length; j++) {
+ switch (statement[j].tok) {
+ case Token.slash:
+ coordinatesAreFractional = true;
+ case Token.rightbrace:
+ break;
+ }
+ }
+ if (coordinatesAreFractional)
+ evalError("fractional coordinates are not allowed in this context");
+ pt.x = coordinateValue(i);
+ pt.y = coordinateValue(++pcLastExpressionInstruction);
+ pt.z = coordinateValue(++pcLastExpressionInstruction);
+ pt.w = coordinateValue(++pcLastExpressionInstruction);
+ if (statement[++pcLastExpressionInstruction].tok != Token.rightbrace)
+ coordinateExpected();
+ return pt;
+ }
+
+
float coordinateValue(int i) throws ScriptException {
// includes support for fractional coordinates
float val = floatParameter(i++);
@@ -3914,12 +3940,20 @@
viewer.loadShape(JmolConstants.SHAPE_ISOSURFACE);
viewer.setShapeProperty(JmolConstants.SHAPE_ISOSURFACE, "init", null);
boolean colorSeen = false;
+ boolean iHavePlane = false;
int colorRangeStage = 0;
for (int i = 1; i < statementLength; ++i) {
String propertyName = null;
Object propertyValue = null;
Token token = statement[i];
switch (token.tok) {
+ case Token.leftbrace:
+ // {X, Y, Z, W}
+ propertyName = "plane";
+ propertyValue = getPoint4f(i);
+ i = pcLastExpressionInstruction;
+ iHavePlane = true;
+ break;
case Token.identifier:
if (((String) token.value).equalsIgnoreCase("fileIndex")) {
fileIndexPt = i + 1;
@@ -3938,10 +3972,19 @@
.getUnzippedBufferedReaderOrErrorMessageFromName(filename);
if (t instanceof String)
fileNotFoundException(filename + ":" + t);
+ if (iHavePlane) {
+ //dual pass when there is a plane defined
+ viewer.setShapeProperty(JmolConstants.SHAPE_ISOSURFACE,
"bufferedReader",
+ t);
+ t = null;
+ t = viewer.getUnzippedBufferedReaderOrErrorMessageFromName(filename);
+ colorSeen = true;
+ iHavePlane = false;
+ }
propertyName = colorSeen ? "colorReader" : "bufferedReader";
- propertyValue = t;
if (colorSeen && colorRangeStage != 0 && colorRangeStage != 3)
invalidArgument();
+ propertyValue = t;
break;
case Token.decimal:
if (colorRangeStage == 0) {
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-05-25
03:47:48 UTC (rev 5168)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-05-25
05:45:51 UTC (rev 5169)
@@ -79,6 +79,7 @@
import java.util.BitSet;
import java.io.BufferedReader;
import javax.vecmath.Point3f;
+import javax.vecmath.Point4f;
import javax.vecmath.Point3i;
import javax.vecmath.Vector3f;
import javax.vecmath.Matrix3f;
@@ -118,14 +119,18 @@
float cutoff = 0.02f;
boolean rangeDefined = false;
float minRange, maxRange;
+
+ Point4f thePlane;
+
BufferedReader br;
void setProperty(String propertyName, Object value, BitSet bs) {
- //System.out.println("isosurface setProperty: " + propertyName + " = " +
value);
+ System.out.println("isosurface setProperty: " + propertyName + " = " +
value);
if ("init" == propertyName) {
fileIndex = 1;
nBytes = 0;
+ thePlane = null;
super.setProperty("meshID", null, null);
return;
}
@@ -135,6 +140,7 @@
fileIndex = 1;
return;
}
+
if ("bufferedReader" == propertyName) {
br = (BufferedReader) value;
if (currentMesh == null)
@@ -142,6 +148,7 @@
currentMesh.clear("isosurface");
readData(false);
calcVoxelVertexVectors();
+ thePlane = null;
constructTessellatedSurface();
currentMesh.colix = getDefaultColix();
currentMesh.initialize();
@@ -151,6 +158,11 @@
System.out.println("\n" + getJvxlFile(currentMesh, (iHaveColorData ?
"mapped" : "")));
return;
}
+ if ("plane" == propertyName) {
+ thePlane = (Point4f) value;
+ cutoff = 0f;
+ return;
+ }
if ("cutoff" == propertyName) {
cutoff = ((Float) value).floatValue();
return;
@@ -379,6 +391,12 @@
cutoff = 0.5f; // just 0s and 1s here. detail is in the edgeFractions
}
line = "";
+ if (thePlane != null) {
+ if (thePlane.x + thePlane.y + thePlane.z == 0)
+ thePlane.z = 1; //{0 0 0 w} becomes {0 0 1 w}
+ vTemp.set(thePlane.x, thePlane.y, thePlane.z);
+ vTempMag = vTemp.length();
+ }
for (int x = 0; x < voxelCountX; ++x) {
float[][] plane = new float[voxelCountY][];
voxelData[x] = plane;
@@ -387,16 +405,19 @@
plane[y] = strip;
for (int z = 0; z < voxelCountZ; ++z) {
float voxelValue = getNextVoxelValue();
+ if (thePlane != null)
+ voxelValue = calcVoxelPlaneDistance(x, y, z);
strip[z] = voxelValue;
++nDataPoints;
if (isJvxl || isMapData)
continue;
boolean isInside = ((cutoff > 0 && voxelValue >= cutoff)
- || (cutoff < 0 && voxelValue <= cutoff));
+ || (cutoff <= 0 && voxelValue <= cutoff));
if (inside == isInside) {
dataCount++;
} else {
- surfaceData += " " + dataCount;
+ if (dataCount != 0)
+ surfaceData += " " + dataCount;
dataCount = 1;
inside = !inside;
}
@@ -411,6 +432,18 @@
+ " x " + voxelCountZ + " voxels");
}
+ float calcVoxelPlaneDistance(int x, int y, int z) {
+ calcVoxelOrigin(x, y, z);
+ return distancePointToPlane(voxelOrigin, thePlane);
+ }
+
+ final Vector3f vTemp = new Vector3f();
+ float vTempMag;
+ float distancePointToPlane(Point3f pt, Point4f plane) {
+ return (plane.x * pt.x + plane.y * pt.y + plane.z * pt.z + plane.w) /
vTempMag;
+ }
+
+
int nStructureData;
int nEdgeData;
int nColorData;
@@ -418,7 +451,7 @@
float jvxlCutoff;
void readJvxlDefinitionLine(boolean showMsg) throws Exception {
- line = br.readLine(); // skip definition line for now
+ while ((line = br.readLine()).length() == 0 || line.charAt(0) == '#') {}
if (showMsg)
System.out.println("reading jvxl data set: " + line);
jvxlCutoff = parseFloat(line);
@@ -554,7 +587,7 @@
+ offset.z];
vertexValues[i] = vertexValue;
if ((cutoff > 0 && vertexValue >= cutoff)
- || (cutoff < 0 && vertexValue <= cutoff))
+ || (cutoff <= 0 && vertexValue <= cutoff))
insideMask |= 1 << i;
}
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