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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 java.io.DataInputStream;
import java.io.BufferedReader;
import org.jmol.viewer.Viewer;
import org.jmol.util.Logger;
import javajs.util.Rdr;
import javajs.util.SB;
class Dsn6BinaryReader extends MapFileReader {
/*
* DSN6 map file reader.
*
* http://eds.bmc.uu.se/eds/
*
* Also referred to as "O" format
*
* see http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/dsn6plugin_8C-source.html
*
*/
Dsn6BinaryReader(){}
@Override
void init2(SurfaceGenerator sg, BufferedReader brNull) {
init2MFR(sg, br);
binarydoc = newBinaryDocument();
Object[] o2 = (Object[]) sg.getReaderData();
String fileName = (String) o2[0];
String data = (String) o2[1];
if (data == null)
binarydoc.setStream(sg.atomDataServer.getBufferedInputStream(fileName), true);
else
binarydoc.setStreamData(new DataInputStream(Rdr.getBIS(data.getBytes())), true);
// data are HIGH on the inside and LOW on the outside
if (params.thePlane == null)
params.insideOut = !params.insideOut;
nSurfaces = 1;
}
private float byteFactor;
private int xyCount;
private int nBrickX, nBrickY;
private int brickLayerVoxelCount;
private int brickLayerByteCount;
private int brickRowByteCount;
private byte[] brickLayer;
@Override
protected void readParameters() throws Exception {
short[] header = new short[19];
for (int i = 0; i < 19; i++)
header[i] = binarydoc.readShort();
if (header[18] != 100) {
binarydoc.setStream(null, false);
for (int i = 0; i < 19; i++)
header[i] = binarydoc.swapBytesS(header[i]);
}
nxyzStart[0] = header[0];
nxyzStart[1] = header[1];
nxyzStart[2] = header[2];
nx = header[3]; // CCP4 "extent[0-2]"
ny = header[4];
nz = header[5];
na = header[6]; // CCP4 "grid[0-2]"
nb = header[7];
nc = header[8];
a = header[9];
b = header[10];
c = header[11];
alpha = header[12];
beta = header[13];
gamma = header[14];
float header16 = header[15]; // 100 * 255 / (dmax - dmin)
float header17 = header[16]; // -255dmin / (dmax - dmin)
float scalingFactor = header[17];
float header19 = header[18];
maps = 3;
mapr = 2;
mapc = 1;
// range parameters are adjusted to be short integers
//
// original: byte range b from 3 to 253 for data values m to M
// [ref: http://www.uoxray.uoregon.edu/tnt/manual/node104.html]
//
// value = [ (b - 3) / 250 ] (M - m) + m
// = [ b - 3 ] * (M - m) / 250 + m
// = [ b - 3 + m * 250 / (M - m) ] * (M - m) / 250
// = [ b - (3 (M - m) - 250 m) / (M - m) ] * (M - m) / 250
// = [ b - (3M - 253m) / (M - m) ] * (M - m) / 250
// = [ b - header17 ] * header19 / header16
//
// where header16 = 100 * 250 / (M - m)
// and header17 = (3M - 253m) / (M - m)
// and header19 = 100
//
// Comment: Perhaps, but what it is actually is simply this:
// [ref: empirical fit to CCP4 and XPLOR data from Uppsala server]
//
// value = [ b / 255 ] (M - m) + m
//
// That is, we are just scaling min to max allowing for a range of 255 byte values.
// So then what we REALLY have is this:
//
// value = [ b / 255 ] (M - m) + m
// = [ b ] * (M - m) / 255 + m
// = [ b + m * 255 / (M - m) ] * (M - m) / 255
// = [ b - (-255 m) / (M - m) ] * (M - m) / 255
// = [ b - header17 ] * header19 / header16
//
// where header16 = 100 * 255 / (M - m)
// and header17 = -255m / (M - m)
// and header19 = 100
//
// If you ask me, this is rather odd, because you
// then have restricted the resolution to only 255 possible values.
// Is the raw data really that low resolution?
// Note that this format has a minimum range limitation of 0.389 = 25500 / 0x10000
// and also a severe limitation in m / (M - m), which very quickly loses precision
// when m is small or (M - m) is large.
//
// In any case, what we do here is simply to
// calculate min and max from headers 16, 17, and 19,
// and then just use:
//
// value = min + b * byteFactor
//
// where byteFactor = (M - m) / 255
//
// Just seems simpler to me. Bob Hanson 2/2010
dmin = (0 - header17) * header19 / header16;
dmax = (255 - header17) * header19 / header16;
drange = dmax - dmin;
byteFactor = drange / 255;
// just to satisfy my curiosity:
float dminError1 = (0 - header17 - 0.5f) * header19 / (header16 - 0.5f);
float dminError2 = (0 - header17 + 0.5f) * header19 / (header16 + 0.5f);
float dmaxError1 = (255 - header17 - 0.5f) * header19 / (header16 - 0.5f);
float dmaxError2 = (255 - header17 + 0.5f) * header19 / (header16 + 0.5f);
float dminError = Math.round((dminError2 - dminError1) / 0.002f) * 0.001f;
float dmaxError = Math.round((dmaxError2 - dmaxError1) / 0.002f) * 0.001f;
Logger.info("DNS6 dmin,dmax = " + dmin + "+/-" + dminError + "," + dmax + "+/-" + dmaxError);
a /= scalingFactor;
b /= scalingFactor;
c /= scalingFactor;
alpha /= scalingFactor;
beta /= scalingFactor;
gamma /= scalingFactor;
binarydoc.seek(0x200);
getVectorsAndOrigin();
setCutoffAutomatic();
xyCount = nx * ny;
brickLayerVoxelCount = xyCount * 8;
// byte blocks are 8 layers of 8x8 voxels, with remainders
nBrickX = (nx + 7) / 8;
nBrickY = (ny + 7) / 8;
brickRowByteCount = nBrickX * 512;
brickLayerByteCount = brickRowByteCount * nBrickY;
brickLayer = new byte[brickLayerByteCount];
jvxlFileHeaderBuffer = new SB();
jvxlFileHeaderBuffer.append("DNS6/O progressive brick data reader\n");
jvxlFileHeaderBuffer
.append("see http://www.uoxray.uoregon.edu/tnt/manual/node104.html\n");
}
private int pt;
private void readBrickLayer() throws Exception {
/*
* Read one full layer of nBrickX*nBrickY 8x8x8 "bricks".
*
*/
binarydoc.readByteArray(brickLayer, 0, brickLayerByteCount);
pt = 0;
nBytes = binarydoc.getPosition();
//System.out.println("DNs6B reader: " + nBytes);
}
private float getBrickValue(int pt) {
/*
* pt runs from [0, n), where n is the number of voxels in a layer of bricks
* But we are running at a specific z through the xy plane, rapidly throuch x.
* You can think of the strips of data being laid out in this order:
*
* brick 0,0,0:
* z = 0, y = 0, x [0-7]
* ...
* z = 0, y = 7, x [0-7]
* z = 1, y = 0, x [0-7]
* ...
* z = 7, y = 7, x [0-7]
*
* brick 0,0,8:
* z = 0, y = 0, x [8-15]
* ...
* z = 0, y = 7, x [8-15]
* z = 1, y = 0, x [8-15]
* ...
* z = 7, y = 7, x [8-15]
*
* So we need to reconstruct from the pointer x, y, and z.
*
*/
// within the data:
int x = pt % nx;
int y = (pt / nx) % ny;
int z = pt / xyCount;
// within the brick:
int brickX = x % 8;
int brickY = y % 8;
int brickZ = z % 8;
// brick pointers:
int bX = x / 8;
int bY = y / 8;
// brick row brick col
int bPt = bY * 512 * nBrickX + bX * 512 + brickZ * 64 + brickY * 8 + brickX;
// reversing byte order:
if (bPt % 2 == 0)
bPt++;
else
bPt--;
// bytes read can be negative
float value = (brickLayer[bPt] + 256) % 256;
return dmin + value * byteFactor;
}
@Override
protected float nextVoxel() throws Exception {
if ((pt % brickLayerVoxelCount) == 0)
readBrickLayer();
return getBrickValue(pt++);
}
@Override
protected void skipData(int nPoints) throws Exception {
for (int i = 0; i < nPoints; i++)
binarydoc.readByte();
}
}