Revision: 5146
Author: hansonr
Date: 2006-05-19 14:09:40 -0700 (Fri, 19 May 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5146&view=rev
Log Message:
-----------
bob200603 isosurface
-adds fileindex option to isosurface command for reading files with multiple
orbitals.
-adds empty string "" default filename is current data file. Could be "that or
previously read isosurface file?"
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 2006-05-19
14:28:45 UTC (rev 5145)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-05-19
21:09:40 UTC (rev 5146)
@@ -3877,8 +3877,9 @@
}
void isosurface() throws ScriptException {
+ int fileIndexPt = 0;
viewer.loadShape(JmolConstants.SHAPE_ISOSURFACE);
- viewer.setShapeProperty(JmolConstants.SHAPE_ISOSURFACE, "meshID", null);
+ viewer.setShapeProperty(JmolConstants.SHAPE_ISOSURFACE, "init", null);
boolean colorSeen = false;
int colorRangeStage = 0;
for (int i = 1; i < statementLength; ++i) {
@@ -3887,13 +3888,19 @@
Token token = statement[i];
switch (token.tok) {
case Token.identifier:
+ if (((String)token.value).equalsIgnoreCase("fileIndex")) {
+ fileIndexPt = i + 1;
+ break;
+ }
propertyValue = token.value;
- // fall into
case Token.all:
propertyName = "meshID";
break;
case Token.string:
String filename = (String)token.value;
+ if (filename.length() == 0)
+ filename = viewer.getFullPathName();
+ System.out.println("reading isosurface data from " + filename);
Object t =
viewer.getUnzippedBufferedReaderOrErrorMessageFromName(filename);
if (t instanceof String)
@@ -3911,6 +3918,13 @@
}
// fall into
case Token.integer:
+ if (i == fileIndexPt) {
+ if (token.tok != Token.integer)
+ integerExpected();
+ propertyName = "fileIndex";
+ propertyValue = new Integer(token.intValue);
+ break;
+ }
if (colorRangeStage == 0 || colorRangeStage >= 3)
invalidArgument();
propertyName = colorRangeStage == 1 ? "rangeMin" : "rangeMax";
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-05-19
14:28:45 UTC (rev 5145)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-05-19
21:09:40 UTC (rev 5146)
@@ -75,6 +75,7 @@
float[][][] voxelData;
int edgePointCount = 0;
+ int fileIndex = 0; //one-based
Point3f[] edgePoints;
float cutoff = 0.02f;
@@ -82,14 +83,22 @@
float minRange, maxRange;
void setProperty(String propertyName, Object value, BitSet bs) {
+ if ("init" == propertyName) {
+ fileIndex = 1;
+ super.setProperty("meshID", null, null);
+ return;
+ }
+ if ("fileIndex" == propertyName) {
+ fileIndex= ((Integer)value).intValue();
+ if (fileIndex < 1) fileIndex = 1;
+ return;
+ }
if ("bufferedReader" == propertyName) {
BufferedReader br = (BufferedReader)value;
if (currentMesh == null)
allocMesh(null);
currentMesh.clear("isosurface");
- readVolumetricHeader(br);
- calcVolumetricMatrix();
- readVolumetricData(br);
+ readData(br);
calcVoxelVertexVectors();
constructTessellatedSurface();
currentMesh.colix = getDefaultColix();
@@ -117,11 +126,9 @@
return;
}
if ("colorReader" == propertyName) {
+ System.out.println("colorReader seen!");
BufferedReader br = (BufferedReader)value;
- System.out.println("colorReader seen!");
- readVolumetricHeader(br);
- calcVolumetricMatrix();
- readVolumetricData(br);
+ readData(br);
if (! rangeDefined) {
minRange = getMinMappedValue();
maxRange = getMaxMappedValue();
@@ -134,7 +141,17 @@
}
super.setProperty(propertyName, value, bs);
}
-
+
+ void readData(BufferedReader br) {
+ int nSurfaces = readVolumetricHeader(br);
+ if (nSurfaces < fileIndex) {
+ System.out.println("not enough surfaces in file -- resetting fileIndex
to " + nSurfaces);
+ fileIndex = nSurfaces;
+ }
+ calcVolumetricMatrix();
+ readVolumetricData(br);
+ }
+
void calcVolumetricMatrix() {
for (int i = 3; --i >= 0; )
volumetricMatrix.setColumn(i, volumetricVectors[i]);
@@ -189,13 +206,13 @@
// file reading stuff
////////////////////////////////////////////////////////////////
- void readVolumetricHeader(BufferedReader br) {
+ int readVolumetricHeader(BufferedReader br) {
try {
readTitleLines(br);
readAtomCountAndOrigin(br);
readVoxelVectors(br);
readAtoms(br);
- readExtraLine(br);
+ return readExtraLine(br);
} catch (Exception e) {
e.printStackTrace();
throw new NullPointerException();
@@ -265,19 +282,19 @@
}
}
- void readExtraLine(BufferedReader br) throws Exception {
- if (negativeAtomCount)
- br.readLine();
+ int readExtraLine(BufferedReader br) throws Exception {
+ return (negativeAtomCount ? parseInt(br.readLine()) : 1);
}
void readVoxelData(BufferedReader br) throws Exception {
- System.out.println("entering readVoxelData");
+ System.out.println("entering readVoxelData for fileIndex = " + fileIndex);
String line = "";
ichNextParse = 0;
int voxelCountX = voxelCounts[0];
int voxelCountY = voxelCounts[1];
int voxelCountZ = voxelCounts[2];
voxelData = new float[voxelCountX][][];
+ skipData(br, (fileIndex - 1) * voxelCountX * voxelCountY * voxelCountZ);
for (int x = 0; x < voxelCountX; ++x) {
float[][] plane = new float[voxelCountY][];
voxelData[x] = plane;
@@ -302,6 +319,35 @@
" x " + voxelCountZ + " voxels");
}
+ void skipData(BufferedReader br, int n) throws Exception {
+ if (n == 0)
+ return;
+ System.out.println("skipping " + n + " datapoints");
+ String line = "";
+ int i=0;
+ while (i < n) {
+ line = br.readLine();
+ int c = countData(line);
+ System.out.println(c + " " + i);
+ i += c;
+ }
+ }
+
+ int countData(String str) {
+ int ich = 0;
+ int count = 0;
+ int ichMax = str.length();
+ char ch;
+ while (ich < ichMax) {
+ while (ich < ichMax && ((ch = str.charAt(ich)) == ' ' || ch == '\t'))
+ ++ich;
+ if (ich < ichMax)
+ ++count;
+ while (ich < ichMax && ((ch = str.charAt(ich)) != ' ' && ch != '\t'))
+ ++ich;
+ }
+ return count;
+ }
////////////////////////////////////////////////////////////////
// marching cube stuff
////////////////////////////////////////////////////////////////
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
-------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
Jmol-commits mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-commits
