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[Jmol-commits] SF.net SVN: jmol: [7307] trunk/Jmol/src/org/openscience/jvxl/readers
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From: <ha...@us...> - 2007-04-02 00:27:30
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Revision: 7307
http://svn.sourceforge.net/jmol/?rev=7307&view=rev
Author: hansonr
Date: 2007-04-01 17:27:27 -0700 (Sun, 01 Apr 2007)
Log Message:
-----------
JVXL refactoring.
Modified Paths:
--------------
trunk/Jmol/src/org/openscience/jvxl/readers/JvxlReader.java
trunk/Jmol/src/org/openscience/jvxl/readers/VolumeDataReader.java
trunk/Jmol/src/org/openscience/jvxl/readers/VolumeFileReader.java
trunk/Jmol/src/org/openscience/jvxl/readers/VoxelReader.java
Modified: trunk/Jmol/src/org/openscience/jvxl/readers/JvxlReader.java
===================================================================
--- trunk/Jmol/src/org/openscience/jvxl/readers/JvxlReader.java 2007-04-01 23:06:55 UTC (rev 7306)
+++ trunk/Jmol/src/org/openscience/jvxl/readers/JvxlReader.java 2007-04-02 00:27:27 UTC (rev 7307)
@@ -336,7 +336,7 @@
return dataOut;
}
- float getNextVoxelValue() throws Exception {
+ float getNextVoxelValue(StringBuffer sb) throws Exception {
//called by VolumeFileReader.readVoxelData
@@ -352,8 +352,8 @@
endOfData = true;
nThisValue = 10000;
//throw new NullPointerException();
- } else {
- surfaceData += line + "\n";
+ } else if (sb != null){
+ sb.append(line).append('\n');
}
}
thisInside = !thisInside;
Modified: trunk/Jmol/src/org/openscience/jvxl/readers/VolumeDataReader.java
===================================================================
--- trunk/Jmol/src/org/openscience/jvxl/readers/VolumeDataReader.java 2007-04-01 23:06:55 UTC (rev 7306)
+++ trunk/Jmol/src/org/openscience/jvxl/readers/VolumeDataReader.java 2007-04-02 00:27:27 UTC (rev 7307)
@@ -54,48 +54,32 @@
readPlaneData();
return;
}
+ voxelData = volumeData.voxelData;
+ if (isMapData)
+ return;
+ StringBuffer sb = new StringBuffer();
boolean inside = false;
int dataCount = 0;
-
- voxelData = volumeData.voxelData;
- if (isMapData || params.thePlane != null)
- return;
nDataPoints = 0;
float cutoff = params.cutoff;
boolean isCutoffAbsolute = params.isCutoffAbsolute;
- for (int x = 0; x < nPointsX; ++x) {
- float[][] plane;
- plane = voxelData[x];
- for (int y = 0; y < nPointsY; ++y) {
- float[] strip;
- strip = plane[y];
+ for (int x = 0; x < nPointsX; ++x)
+ for (int y = 0; y < nPointsY; ++y)
for (int z = 0; z < nPointsZ; ++z) {
- float voxelValue;
- voxelValue = strip[z]; //precalculated
++nDataPoints;
- if (inside == isInside(voxelValue, cutoff, isCutoffAbsolute)) {
+ if (inside == isInside(voxelData[x][y][z], cutoff, isCutoffAbsolute)) {
dataCount++;
} else {
if (dataCount != 0)
- surfaceData += " " + dataCount;
+ sb.append(' ').append(dataCount);
dataCount = 1;
inside = !inside;
}
}
- }
- }
- surfaceData += " " + dataCount + "\n";
- jvxlData.jvxlSurfaceData = surfaceData;
+ sb.append(' ').append(dataCount).append('\n');
+ jvxlData.jvxlSurfaceData = sb.toString();
jvxlData.jvxlPlane = params.thePlane;
volumeData.setVoxelData(voxelData);
- }
-
- float getVoxelValue(int x, int y, int z) {
- return volumeData.voxelData[x][y][z];
- }
-
-
+ }
}
-
-
Modified: trunk/Jmol/src/org/openscience/jvxl/readers/VolumeFileReader.java
===================================================================
--- trunk/Jmol/src/org/openscience/jvxl/readers/VolumeFileReader.java 2007-04-01 23:06:55 UTC (rev 7306)
+++ trunk/Jmol/src/org/openscience/jvxl/readers/VolumeFileReader.java 2007-04-02 00:27:27 UTC (rev 7307)
@@ -232,47 +232,59 @@
voxelData = new float[nPointsX][][];
nDataPoints = 0;
line = "";
- float cutoff = params.cutoff;
- boolean isCutoffAbsolute = params.isCutoffAbsolute;
- for (int x = 0; x < nPointsX; ++x) {
- float[][] plane;
- plane = new float[nPointsY][];
- voxelData[x] = plane;
- for (int y = 0; y < nPointsY; ++y) {
- float[] strip;
- strip = new float[nPointsZ];
- plane[y] = strip;
- for (int z = 0; z < nPointsZ; ++z) {
- float voxelValue = getNextVoxelValue();
- strip[z] = voxelValue;
- ++nDataPoints;
- if (isMapData || isJvxl && params.thePlane == null)
- continue;
-
- // update surfaceData
-
- if (inside == isInside(voxelValue, cutoff, isCutoffAbsolute)) {
- dataCount++;
- } else {
- if (dataCount != 0)
- surfaceData += " " + dataCount;
- dataCount = 1;
- inside = !inside;
+ StringBuffer sb = new StringBuffer();
+ boolean collectData = (!isJvxl && params.thePlane == null);
+ if (isMapData || isJvxl && params.thePlane == null) {
+ for (int x = 0; x < nPointsX; ++x) {
+ float[][] plane = new float[nPointsY][];
+ voxelData[x] = plane;
+ for (int y = 0; y < nPointsY; ++y) {
+ float[] strip = new float[nPointsZ];
+ plane[y] = strip;
+ for (int z = 0; z < nPointsZ; ++z) {
+ strip[z] = getNextVoxelValue(sb);
+ ++nDataPoints;
}
}
}
+ } else {
+ float cutoff = params.cutoff;
+ boolean isCutoffAbsolute = params.isCutoffAbsolute;
+ for (int x = 0; x < nPointsX; ++x) {
+ float[][] plane;
+ plane = new float[nPointsY][];
+ voxelData[x] = plane;
+ for (int y = 0; y < nPointsY; ++y) {
+ float[] strip = new float[nPointsZ];
+ plane[y] = strip;
+ for (int z = 0; z < nPointsZ; ++z) {
+ float voxelValue = getNextVoxelValue(sb);
+ strip[z] = voxelValue;
+ ++nDataPoints;
+ if (inside == isInside(voxelValue, cutoff, isCutoffAbsolute)) {
+ dataCount++;
+ } else {
+ if (collectData && dataCount != 0)
+ sb.append(' ').append(dataCount);
+ dataCount = 1;
+ inside = !inside;
+ }
+ }
+ }
+ }
}
- if (!isJvxl)
- surfaceData += " " + dataCount + "\n";
+ //Jvxl getNextVoxelValue records the data read on its own.
+ if (collectData)
+ sb.append(' ').append(dataCount).append('\n');
if (!isMapData) {
- jvxlData.jvxlSurfaceData = (params.thePlane == null ? surfaceData : "");
+ jvxlData.jvxlSurfaceData = sb.toString();
jvxlData.jvxlPlane = params.thePlane;
}
volumeData.setVoxelData(voxelData);
}
- float getNextVoxelValue() throws Exception {
- //overloaded in JvxlReader
+ float getNextVoxelValue(StringBuffer sb) throws Exception {
+ //overloaded in JvxlReader, where sb is appended to
float voxelValue = 0;
if (nSurfaces > 1 && !params.blockCubeData) {
for (int i = 1; i < params.fileIndex; i++)
Modified: trunk/Jmol/src/org/openscience/jvxl/readers/VoxelReader.java
===================================================================
--- trunk/Jmol/src/org/openscience/jvxl/readers/VoxelReader.java 2007-04-01 23:06:55 UTC (rev 7306)
+++ trunk/Jmol/src/org/openscience/jvxl/readers/VoxelReader.java 2007-04-02 00:27:27 UTC (rev 7307)
@@ -133,7 +133,6 @@
int nBytes;
int nDataPoints;
- String surfaceData;
int nPointsX, nPointsY, nPointsZ;
private int edgeCount;
@@ -209,7 +208,6 @@
void initializeVolumetricData() {
nThisValue = 0;
- surfaceData = "";
nPointsX = voxelCounts[0];
nPointsY = voxelCounts[1];
nPointsZ = voxelCounts[2];
@@ -257,8 +255,8 @@
if (inside == isInside(voxelValue, cutoff, isCutoffAbsolute)) {
dataCount++;
} else {
- if (dataCount != 0)
- surfaceData += " " + dataCount;
+ //if (dataCount != 0)
+ //surfaceData += " " + dataCount;
dataCount = 1;
inside = !inside;
}
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