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Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $Author: hansonr $
* $Date: 2007-10-08 22:18:02 -0500 (Mon, 08 Oct 2007) $
* $Revision: 8391 $
*
* Copyright (C) 2003-2005 The Jmol Development Team
*
* 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 Public 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.shapespecial;
import java.util.BitSet;
import java.util.Iterator;
import javax.vecmath.Matrix3f;
import javax.vecmath.Matrix4f;
import javax.vecmath.Point3f;
import javax.vecmath.Point3i;
import javax.vecmath.Vector3f;
import org.jmol.g3d.Graphics3D;
import org.jmol.util.Quadric;
import org.jmol.modelset.Atom;
import org.jmol.shape.Shape;
import org.jmol.shape.ShapeRenderer;
import org.jmol.shapespecial.Ellipsoids.Ellipsoid;
import org.jmol.viewer.JmolConstants;
public class EllipsoidsRenderer extends ShapeRenderer {
private Ellipsoids ellipsoids;
private boolean drawDots, drawArcs, drawAxes, drawFill, drawBall;
private boolean wireframeOnly;
private int dotCount;
private int[] coords;
private Vector3f[] axes;
private final float[] factoredLengths = new float[3];
private int diameter, diameter0;
private int selectedOctant = -1;
private Point3i[] selectedPoints = new Point3i[3];
private int iCutout = -1;
private Matrix3f mat = new Matrix3f();
private Matrix3f mTemp = new Matrix3f();
private Matrix4f mDeriv = new Matrix4f();
private Matrix3f matScreenToCartesian = new Matrix3f();
private Matrix3f matScreenToEllipsoid = new Matrix3f();
private Matrix3f matEllipsoidToScreen = new Matrix3f();
private double[] coef = new double[10];
private final Vector3f v1 = new Vector3f();
private final Vector3f v2 = new Vector3f();
private final Vector3f v3 = new Vector3f();
private final Point3f pt1 = new Point3f();
private final Point3f pt2 = new Point3f();
private final Point3i s0 = new Point3i();
private final Point3i s1 = new Point3i();
private final Point3i s2 = new Point3i();
private int dotScale;
private final static float toRadians = (float) Math.PI/180f;
private final static float[] cossin = new float[36];
static {
for (int i = 5, pt = 0; i <= 90; i += 5) {
cossin[pt++] = (float) Math.cos(i * toRadians);
cossin[pt++] = (float) Math.sin(i * toRadians);
}
}
@Override
protected void render() {
ellipsoids = (Ellipsoids) shape;
if (ellipsoids.madset == null && !ellipsoids.haveEllipsoids)
return;
wireframeOnly = (viewer.getWireframeRotation() && viewer.getInMotion());
drawAxes = viewer.getBooleanProperty("ellipsoidAxes");
drawArcs = viewer.getBooleanProperty("ellipsoidArcs");
drawBall = viewer.getBooleanProperty("ellipsoidBall") && !wireframeOnly;
drawDots = viewer.getBooleanProperty("ellipsoidDots") && !wireframeOnly;
drawFill = viewer.getBooleanProperty("ellipsoidFill") && !wireframeOnly;
fillArc = drawFill && !drawBall;
diameter0 = (int) (((Float) viewer.getParameter("ellipsoidAxisDiameter"))
.floatValue() * 1000);
//perspectiveOn = viewer.getPerspectiveDepth();
/* general logic:
*
*
* 1) octant and DOTS are incompatible; octant preferred over dots
* 2) If not BALL, ARCS, or DOTS, the rendering defaults to AXES
* 3) If DOTS, then turn off ARCS and FILL
*
* note that FILL serves to provide a cut-out for BALL and a
* filling for ARCS
*/
if (drawBall)
drawDots = false;
if (!drawDots && !drawArcs && !drawBall)
drawAxes = true;
if (drawDots) {
drawArcs = false;
drawFill = false;
dotScale = viewer.getDotScale();
}
if (drawDots) {
dotCount = ((Integer) viewer.getParameter("ellipsoidDotCount"))
.intValue();
if (coords == null || coords.length != dotCount * 3)
coords = new int[dotCount * 3];
}
Matrix4f m4 = viewer.getMatrixtransform();
mat.setRow(0, m4.m00, m4.m01, m4.m02);
mat.setRow(1, m4.m10, m4.m11, m4.m12);
mat.setRow(2, m4.m20, m4.m21, m4.m22);
matScreenToCartesian.invert(mat);
Atom[] atoms = modelSet.atoms;
for (int i = modelSet.getAtomCount(); --i >= 0;) {
Atom atom = atoms[i];
if (!atom.isVisible(myVisibilityFlag))
continue;
if (atom.screenZ <= 1)
continue;
Quadric[] ellipsoid2 = atom.getEllipsoid();
if (ellipsoid2 == null)
continue;
for (int j = 0; j < ellipsoid2.length; j++) {
if (ellipsoid2[j] == null || ellipsoids.madset[j] == null || ellipsoids.madset[j][i] == 0)
continue;
colix = Shape.getColix(ellipsoids.colixset[j], i, atom);
if (!g3d.setColix(colix))
continue;
//if (i == 0) System.out.println("ell rend " + j + " " + i + ": " + ellipsoid2[j]);
render1(atom, ellipsoid2[j]);
}
}
if (ellipsoids.haveEllipsoids) {
Iterator e = ellipsoids.htEllipsoids.values().iterator();
while (e.hasNext()) {
Ellipsoid ellipsoid = e.next();
if (ellipsoid.visible && ellipsoid.isValid)
renderEllipsoid(ellipsoid);
}
}
coords = null;
}
private final Point3i[] screens = new Point3i[32];
//private final int[] intensities = new int[32];
private final Point3f[] points = new Point3f[6];
{
for (int i = 0; i < points.length; i++)
points[i] = new Point3f();
for (int i = 0; i < screens.length; i++)
screens[i] = new Point3i();
}
private static int[] axisPoints = {-1, 1, -2, 2, -3, 3};
// octants are sets of three axisPoints references in proper rotation order
// axisPoints[octants[i]] indicates the axis and direction (pos/neg)
private static int[] octants = {
5, 0, 3,
5, 2, 0, //arc
4, 0, 2,
4, 3, 0, //arc
5, 2, 1,
5, 1, 3, //arc
4, 3, 1,
4, 1, 2 //arc
};
private int dx;
private float perspectiveFactor;
private Point3f center;
private void render1(Atom atom, Quadric ellipsoid) {
s0.set(atom.screenX, atom.screenY, atom.screenZ);
boolean isOK = true;
for (int i = 3; --i >= 0;) {
factoredLengths[i] = ellipsoid.lengths[i] * ellipsoid.scale;
if (Float.isNaN(factoredLengths[i]))
isOK = false;
else if (factoredLengths[i] < 0.02f)
factoredLengths[i] = 0.02f; // for extremely flat ellipsoids, we need at least some length
}
axes = ellipsoid.vectors;
if (axes == null) { //isotropic
axes = unitVectors;
}
setMatrices();
//[0] is shortest; [2] is longest
center = atom;
setAxes(1.0f);
if (g3d.isClippedXY(dx + dx, atom.screenX, atom.screenY))
return;
diameter = viewer.scaleToScreen(atom.screenZ, wireframeOnly ? 1 : diameter0);
if (!isOK || drawBall) {
renderBall();
if (!isOK)
return;
if (drawArcs || drawAxes) {
g3d.setColix(viewer.getColixBackgroundContrast());
//setAxes(atom, 1.0f);
if (drawAxes)
renderAxes();
if (drawArcs)
renderArcs(atom);
g3d.setColix(colix);
}
} else {
if (drawAxes)
renderAxes();
if (drawArcs)
renderArcs(atom);
}
if (drawDots)
renderDots(atom);
}
private void setMatrices() {
Quadric.setEllipsoidMatrix(axes, factoredLengths, v1, mat);
// make this screen coordinates to ellisoidal coordinates
matScreenToEllipsoid.mul(mat, matScreenToCartesian);
matEllipsoidToScreen.invert(matScreenToEllipsoid);
//matEllipsoidToScreen.mul(viewer.scaleToScreen(s0.z, 1000));
perspectiveFactor = viewer.scaleToPerspective(s0.z, 1.0f);
matScreenToEllipsoid.mul(1f/perspectiveFactor);
}
private final static Vector3f[] unitVectors = {
JmolConstants.axisX, JmolConstants.axisY, JmolConstants.axisZ};
private final static Vector3f[] unitAxisVectors = {
JmolConstants.axisNX, JmolConstants.axisX,
JmolConstants.axisNY, JmolConstants.axisY,
JmolConstants.axisNZ, JmolConstants.axisZ };
private void setAxes(float f) {
for (int i = 0; i < 6; i++) {
int iAxis = axisPoints[i];
int i012 = Math.abs(iAxis) - 1;
points[i].scaleAdd(f * factoredLengths[i012] * (iAxis < 0 ? -1 : 1),
axes[i012], center);
pt1.set(unitAxisVectors[i]);
pt1.scale(f);
matEllipsoidToScreen.transform(pt1);
screens[i].set((int) (s0.x + pt1.x * perspectiveFactor),
(int) (s0.y + pt1.y * perspectiveFactor), (int) (pt1.z + s0.z));
}
dx = 2 + viewer.scaleToScreen(s0.z,
(int) (f * (Float.isNaN(factoredLengths[2]) ? 1.0 : factoredLengths[2]) * 1000));
}
private void renderAxes() {
if (drawBall && drawFill) {
g3d.fillCylinder(Graphics3D.ENDCAPS_FLAT, diameter, s0,
selectedPoints[0]);
g3d.fillCylinder(Graphics3D.ENDCAPS_FLAT, diameter, s0,
selectedPoints[1]);
g3d.fillCylinder(Graphics3D.ENDCAPS_FLAT, diameter, s0,
selectedPoints[2]);
return;
}
// if (Logger.debugging) {
// g3d.setColix(Graphics3D.RED);
// g3d.fillCylinder(Graphics3D.ENDCAPS_FLAT, diameter, screens[0],
// screens[1]);
// g3d.setColix(Graphics3D.GREEN);
// g3d.fillCylinder(Graphics3D.ENDCAPS_FLAT, diameter, screens[2],
// screens[3]);
// g3d.setColix(Graphics3D.BLUE);
// g3d.fillCylinder(Graphics3D.ENDCAPS_FLAT, diameter, screens[4],
// screens[5]);
// g3d.setColix(colix);
// } else {
g3d.fillCylinder(Graphics3D.ENDCAPS_FLAT, diameter, screens[0],
screens[1]);
g3d.fillCylinder(Graphics3D.ENDCAPS_FLAT, diameter, screens[2],
screens[3]);
g3d.fillCylinder(Graphics3D.ENDCAPS_FLAT, diameter, screens[4],
screens[5]);
// }
}
private void renderDots(Point3f ptAtom) {
for (int i = 0; i < coords.length;) {
float fx = (float) Math.random();
float fy = (float) Math.random();
fx *= (Math.random() > 0.5 ? -1 : 1);
fy *= (Math.random() > 0.5 ? -1 : 1);
float fz = (float) Math.sqrt(1 - fx * fx - fy * fy);
if (Float.isNaN(fz))
continue;
fz = (Math.random() > 0.5 ? -1 : 1) * fz;
pt1.scaleAdd(fx * factoredLengths[0], axes[0], ptAtom);
pt1.scaleAdd(fy * factoredLengths[1], axes[1], pt1);
pt1.scaleAdd(fz * factoredLengths[2], axes[2], pt1);
viewer.transformPoint(pt1, s1);
coords[i++] = s1.x;
coords[i++] = s1.y;
coords[i++] = s1.z;
}
g3d.drawPoints(dotCount, coords, dotScale);
}
private void renderArcs(Point3f ptAtom) {
if (g3d.drawEllipse(ptAtom, points[0], points[2], fillArc, wireframeOnly)) {
g3d.drawEllipse(ptAtom, points[2], points[5], fillArc, wireframeOnly);
g3d.drawEllipse(ptAtom, points[5], points[0], fillArc, wireframeOnly);
return;
}
for (int i = 1; i < 8; i += 2) {
int pt = i*3;
renderArc(ptAtom, octants[pt], octants[pt + 1]);
renderArc(ptAtom, octants[pt + 1], octants[pt + 2]);
renderArc(ptAtom, octants[pt + 2], octants[pt]);
}
}
private boolean fillArc;
private BitSet bsTemp = new BitSet();
private void renderArc(Point3f ptAtom, int ptA, int ptB) {
v1.set(points[ptA]);
v1.sub(ptAtom);
v2.set(points[ptB]);
v2.sub(ptAtom);
float d1 = v1.length();
float d2 = v2.length();
v1.normalize();
v2.normalize();
v3.cross(v1, v2);
pt1.set(points[ptA]);
s1.set(screens[ptA]);
short normix = Graphics3D.get2SidedNormix(v3, bsTemp);
if (!fillArc && !wireframeOnly)
screens[6].set(s1);
for (int i = 0, pt = 0; i < 18; i++, pt += 2) {
pt2.scaleAdd(cossin[pt] * d1, v1, ptAtom);
pt2.scaleAdd(cossin[pt + 1] * d2, v2, pt2);
viewer.transformPoint(pt2, s2);
if (fillArc)
g3d.fillTriangle(s0, colix, normix, s1, colix, normix, s2, colix,
normix);
else if (wireframeOnly)
g3d.fillCylinder(Graphics3D.ENDCAPS_FLAT, diameter, s1, s2);
else
screens[i + 7].set(s2);
pt1.set(pt2);
s1.set(s2);
}
if (!fillArc && !wireframeOnly)
for (int i = 0; i < 18; i++) {
g3d.fillHermite(5, diameter, diameter, diameter,
screens[i == 0 ? i + 6 : i + 5],
screens[i + 6],
screens[i + 7],
screens[i == 17 ? i + 7 : i + 8]);
}
}
protected void renderEllipsoid(Ellipsoid ellipsoid) {
axes = ellipsoid.axes;
for (int i = 0; i < 3; i++)
factoredLengths[i] = ellipsoid.lengths[i];
viewer.transformPoint(ellipsoid.center, s0);
setMatrices();
center = ellipsoid.center;
setAxes(1);
colix = ellipsoid.colix;
if (!g3d.setColix(colix))
return;
renderBall();
}
protected void renderBall() {
setSelectedOctant();
// get equation and differential
Quadric.getEquationForQuadricWithCenter(s0.x, s0.y, s0.z,
matScreenToEllipsoid, v1, mTemp, coef, mDeriv);
g3d.fillEllipsoid(center, points, s0.x, s0.y, s0.z, dx + dx, matScreenToEllipsoid,
coef, mDeriv, selectedOctant, selectedOctant >= 0 ? selectedPoints : null);
}
private void setSelectedOctant() {
int zMin = Integer.MAX_VALUE;
selectedOctant = -1;
iCutout = -1;
if (drawFill) {
for (int i = 0; i < 8; i++) {
int ptA = octants[i * 3];
int ptB = octants[i * 3 + 1];
int ptC = octants[i * 3 + 2];
int z = screens[ptA].z + screens[ptB].z + screens[ptC].z;
if (z < zMin) {
zMin = z;
iCutout = i;
}
}
//TODO -- adjust x and y for perspective?
s1.set(selectedPoints[0] = screens[octants[iCutout * 3]]);
s1.add(selectedPoints[1] = screens[octants[iCutout * 3 + 1]]);
s1.add(selectedPoints[2] = screens[octants[iCutout * 3 + 2]]);
s1.scaleAdd(-3, s0, s1);
pt1.set(s1.x, s1.y, s1.z);
matScreenToEllipsoid.transform(pt1);
selectedOctant = Quadric.getOctant(pt1);
}
}
}