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Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $Author: hansonr $
* $Date: 2007-03-30 11:40:16 -0500 (Fri, 30 Mar 2007) $
* $Revision: 7273 $
*
* Copyright (C) 2007 Miguel, Bob, Jmol Development
*
* Contact: [email protected]
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.jmol.jvxl.readers;
import javax.vecmath.Point4f;
import java.io.BufferedReader;
import org.jmol.util.Escape;
import org.jmol.util.Logger;
import org.jmol.util.Parser;
import org.jmol.g3d.Graphics3D;
import org.jmol.jvxl.data.JvxlCoder;
public class JvxlReader extends JvxlXmlReader {
// 1.4 adds -nContours to indicate contourFromZero for MEP data mapped onto planes
// 2.0 adds vertex/triangle compression when no grid is present
// Jmol 11.7.25 -- recoded so that we do not create voxelData[nx][ny][nz] and instead
// simply create a BitSet of length nx * ny * nz. This saves memory hugely.
// 2.1 adds JvxlXmlReader
JvxlReader(SurfaceGenerator sg, BufferedReader br) {
super(sg, br);
isXmlFile = false;
JVXL_VERSION = "2.0";
}
// // methods used for reading any file format, but creating a JVXL file
// ///////////reading the format///////////
@Override
protected void readParameters() throws Exception {
jvxlFileHeaderBuffer = new StringBuffer(skipComments(false));
if (line == null || line.length() == 0)
line = "Line 1";
jvxlFileHeaderBuffer.append(line).append('\n');
if (readLine() == null || line.length() == 0)
line = "Line 2";
jvxlFileHeaderBuffer.append(line).append('\n');
jvxlFileHeaderBuffer.append(skipComments(false));
String atomLine = line;
String[] tokens = Parser.getTokens(atomLine, 0);
isXLowToHigh = false;
negativeAtomCount = true;
atomCount = 0;
if (tokens[0] == "-0") {
} else if (tokens[0].charAt(0) == '+') {
isXLowToHigh = true;
atomCount = parseInt(tokens[0].substring(1));
} else {
atomCount = -parseInt(tokens[0]);
}
if (atomCount == Integer.MIN_VALUE)
return;
volumetricOrigin.set(parseFloat(tokens[1]), parseFloat(tokens[2]),
parseFloat(tokens[3]));
isAngstroms = VolumeFileReader.checkAtomLine(isXLowToHigh, isAngstroms,
null, atomLine, jvxlFileHeaderBuffer);
if (!isAngstroms)
volumetricOrigin.scale(ANGSTROMS_PER_BOHR);
readVoxelVector(0);
readVoxelVector(1);
readVoxelVector(2);
skipComments(true);
for (int i = 0; i < atomCount; ++i)
jvxlFileHeaderBuffer.append(readLine() + "\n");
Logger.info("Reading extra JVXL information line: " + line);
nSurfaces = parseInt(line);
if (!(isJvxl = (nSurfaces < 0)))
return;
nSurfaces = -nSurfaces;
Logger.info("jvxl file surfaces: " + nSurfaces);
int ich;
if ((ich = parseInt()) == Integer.MIN_VALUE) {
Logger.info("using default edge fraction base and range");
} else {
edgeFractionBase = ich;
edgeFractionRange = parseInt();
}
if ((ich = parseInt()) == Integer.MIN_VALUE) {
Logger.info("using default color fraction base and range");
} else {
colorFractionBase = ich;
colorFractionRange = parseInt();
}
cJvxlEdgeNaN = (char)(edgeFractionBase + edgeFractionRange);
}
@Override
protected String jvxlReadData(String type, int nPoints) {
String str = "";
try {
while (str.length() < nPoints) {
readLine();
str += JvxlCoder.jvxlUncompressString(line);
}
} catch (Exception e) {
Logger.error("Error reading " + type + " data " + e);
throw new NullPointerException();
}
return str;
}
@Override
protected void gotoData(int n, int nPoints) throws Exception {
//called by VolumeFileReader.readVoxelData
if (n > 0)
Logger.info("skipping " + n + " data sets, " + nPoints + " points each");
vertexDataOnly = jvxlData.vertexDataOnly = (nPoints == 0);
for (int i = 0; i < n; i++) {
jvxlReadDefinitionLine(true);
Logger.info("JVXL skipping: jvxlSurfaceDataCount=" + surfaceDataCount
+ " jvxlEdgeDataCount=" + edgeDataCount
+ " jvxlDataIsColorMapped=" + jvxlDataIsColorMapped);
jvxlSkipData(nPoints, true);
}
jvxlReadDefinitionLine(true);
}
private void jvxlReadDefinitionLine(boolean showMsg) throws Exception {
// params values come from user adding options to the isosurface command
// jvxlData values are from this file
String comment = skipComments(true);
if (showMsg)
Logger.info("reading jvxl data set: " + comment + line);
haveContourData = (comment.indexOf("+contourlines") >= 0);
jvxlCutoff = parseFloat(line);
Logger.info("JVXL read: cutoff " + jvxlCutoff);
// optional comment line for compatibility with earlier Jmol versions:
// #+contourlines
// cutoff nInts (+/-)bytesEdgeData (+/-)bytesColorData
// param1 param2 param3
// | | |
// when | | > 0 ==> jvxlDataIsColorMapped
// when | | == -1 ==> not color mapped
// when | | < -1 ==> jvxlDataIsPrecisionColor
// when == -1 && == -1 ==> noncontoured plane
// when == -1 && == -2 ==> contourable plane
// when < -1* && > 0 ==> contourable functionXY
// when > 0 && < 0 ==> jvxlDataisBicolorMap
// * nInts saved as -1 - nInts
// it's possible that a plane will not be contoured (-1 -1) when it is a solid color.
// why you would want to save this as JVXL is another question.
// instead, we just set "contour 1" to indicate just one contour to demo that.
// In addition, now we consider contouring functionXY, so in that case we would
// have surface data, edge data, and color data
int param1 = parseInt();
int param2 = parseInt();
int param3 = parseInt();
if (param3 == Integer.MIN_VALUE || param3 == -1)
param3 = 0;
if (param1 == -1) {
// a plane is defined
try {
params.thePlane = new Point4f(parseFloat(), parseFloat(), parseFloat(),
parseFloat());
} catch (Exception e) {
Logger
.error("Error reading 4 floats for PLANE definition -- setting to 0 0 1 0 (z=0)");
params.thePlane = new Point4f(0, 0, 1, 0);
}
Logger.info("JVXL read: plane " + params.thePlane);
if (param2 == -1 && param3 < 0)
param3 = -param3;
//error in some versions of Jmol. (fixed in 11.3.54)
} else {
params.thePlane = null;
}
if (param1 < 0 && param2 != -1) {
// contours are defined (possibly overridden -- this is just a display option
// could be plane or functionXY
params.isContoured = (param3 != 0);
int nContoursRead = parseInt();
if (nContoursRead == Integer.MIN_VALUE) {
if (line.charAt(next[0]) == '[') {
jvxlData.contourValues = params.contoursDiscrete = parseFloatArray();
Logger.info("JVXL read: contourValues " + Escape.escapeArray(jvxlData.contourValues));
jvxlData.contourColixes = params.contourColixes = Graphics3D.getColixArray(getNextQuotedString());
jvxlData.contourColors = Graphics3D.getHexCodes(jvxlData.contourColixes);
Logger.info("JVXL read: contourColixes " + jvxlData.contourColors);
params.nContours = jvxlData.contourValues.length;
}
} else {
if (nContoursRead < 0) {
nContoursRead = -1 - nContoursRead;
params.contourFromZero = false; //MEP data to complete the plane
}
if (nContoursRead != 0 && params.nContours == 0) {
params.nContours = nContoursRead;
Logger.info("JVXL read: contours " + params.nContours);
}
}
} else {
params.isContoured = false;
}
jvxlData.isJvxlPrecisionColor = (param1 == -1 && param2 == -2
|| param3 < 0);
params.isBicolorMap = (param1 > 0 && param2 < 0);
jvxlDataIsColorMapped = (param3 != 0);
jvxlDataIs2dContour = (jvxlDataIsColorMapped && params.isContoured);
if (params.isBicolorMap || params.colorBySign)
jvxlCutoff = 0;
surfaceDataCount = (param1 < -1 ? -1 - param1 : param1 > 0 ? param1 : 0);
//prior to JVXL 1.1 (4/2007), this number counts the bytes of integer data.
//after that, the number of integers, for the progressive reader
if (param1 == -1)
edgeDataCount = 0; //plane
else
edgeDataCount = (param2 < -1 ? -param2 : param2 > 0 ? param2 : 0);
colorDataCount = (params.isBicolorMap ? -param2 : param3 < -1 ? -param3
: param3 > 0 ? param3 : 0);
if (params.colorBySign)
params.isBicolorMap = true;
float dataMin = Float.NaN;
float dataMax = Float.NaN;
float red = Float.NaN;
float blue = Float.NaN;
boolean insideOut = (line.indexOf("insideOut") >= 0);
if (jvxlDataIsColorMapped) {
dataMin = parseFloat();
dataMax = parseFloat();
red = parseFloat();
blue = parseFloat();
}
jvxlSetColorRanges(dataMin, dataMax, red, blue, insideOut);
}
@Override
protected void readSurfaceData(boolean isMapDataIgnored) throws Exception {
thisInside = !params.isContoured;
if (readSurfaceData())
return;
readVolumeFileSurfaceData();
}
@Override
protected void jvxlSkipData(int nPoints, boolean doSkipColorData)
throws Exception {
// surfaceDataCount is quantitatively unreliable in pre-4/2007 versions (Jvxl 1.0)
// so we just add them all up -- they must sum to nX * nY * nZ points
if (surfaceDataCount > 0) // unreliable in pre-4/2007 versions (Jvxl 1.0)
jvxlSkipDataBlock(nPoints, true);
if (edgeDataCount > 0)
jvxlSkipDataBlock(edgeDataCount, false);
if (jvxlDataIsColorMapped && doSkipColorData)
jvxlSkipDataBlock(colorDataCount, false);
}
private void jvxlSkipDataBlock(int nPoints, boolean isInt) throws Exception {
int n = 0;
while (n < nPoints) {
readLine();
n += (isInt ? countData(line) : JvxlCoder.jvxlUncompressString(line).length());
}
}
private int countData(String str) {
int count = 0;
int n = parseInt(str);
while (n != Integer.MIN_VALUE) {
count += n;
n = parseIntNext(str);
}
return count;
}
}