Revision: 20465
http://sourceforge.net/p/jmol/code/20465
Author: hansonr
Date: 2015-04-30 13:17:17 +0000 (Thu, 30 Apr 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.13_2015.04.30"
bug fix: POV-Ray fixed for perspective and orthographic cameras using new
z-depth formula.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/export/Export3D.java
trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
trunk/Jmol/src/org/jmol/export/_TachyonExporter.java
trunk/Jmol/src/org/jmol/export/__CartesianExporter.java
trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java
trunk/Jmol/src/org/jmol/export/___Exporter.java
trunk/Jmol/src/org/jmol/g3d/CircleRenderer.java
trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
Modified: trunk/Jmol/src/org/jmol/export/Export3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/Export3D.java 2015-04-30 03:09:00 UTC
(rev 20464)
+++ trunk/Jmol/src/org/jmol/export/Export3D.java 2015-04-30 13:17:17 UTC
(rev 20465)
@@ -548,10 +548,8 @@
// from Draw arrow and NucleicMonomer
if (diameter <= 0)
return;
- if (!exporter.isCartesian) {
- ptA.set(pointA.x, pointA.y, pointA.z);
- ptB.set(pointB.x, pointB.y, pointB.z);
- }
+ ptA.set(pointA.x, pointA.y, pointA.z);
+ ptB.set(pointB.x, pointB.y, pointB.z);
exporter.fillCylinderScreen(colix, endcaps, diameter, ptA, ptB, pt0f, pt1f,
radius);
}
@@ -651,7 +649,7 @@
// shouldn't be here, because that uses renderIsosurface
return;
}
- exporter.fillTriangle(colixA, pA, pB, pC, false, false);
+ exporter.fillTriangle(colixA, pA, pB, pC, false);
}
@Override
@@ -666,7 +664,7 @@
ptA.set(pointA.x, pointA.y, pointA.z);
ptB.set(pointB.x, pointB.y, pointB.z);
ptC.set(pointC.x, pointC.y, pointC.z);
- exporter.fillTriangle(colixA, ptA, ptB, ptC, false, false);
+ exporter.fillTriangle(colixA, ptA, ptB, ptC, false);
}
@Override
@@ -678,27 +676,23 @@
ptA.set(xpointA, ypointA, zpointA);
ptB.set(xpointB, ypointB, zpointB);
ptC.set(xpointC, ypointC, zpointC);
- exporter.fillTriangle(colix, ptA, ptB, ptC, true, false);
+ exporter.fillTriangle(colix, ptA, ptB, ptC, true);
}
@Override
public void fillTriangle3f(P3 pointA, P3 pointB, P3 pointC, boolean
setNoisy) {
// rockets
- exporter.fillTriangle(colix, pointA, pointB, pointC, false, false);
+ exporter.fillTriangle(colix, pointA, pointB, pointC, false);
}
@Override
public void fillTriangle3i(P3i screenA, P3i screenB, P3i screenC, T3 ptA0,
T3 ptB0, T3 ptC0, boolean doShade) {
// cartoon only, for nucleic acid bases
- if (exporter.isCartesian) {
- exporter.fillTriangle(colix, ptA0, ptB0, ptC0, true, true);
- } else {
ptA.set(screenA.x, screenA.y, screenA.z);
ptB.set(screenB.x, screenB.y, screenB.z);
ptC.set(screenC.x, screenC.y, screenC.z);
- exporter.fillTriangle(colix, ptA, ptB, ptC, true, false);
- }
+ exporter.fillTriangle(colix, ptA, ptB, ptC, true);
}
/*
@@ -728,8 +722,8 @@
@Override
public void fillQuadrilateral(P3 pointA, P3 pointB, P3 pointC, P3 pointD) {
// hermite, rockets, cartoons
- exporter.fillTriangle(colix, pointA, pointB, pointC, false, false);
- exporter.fillTriangle(colix, pointA, pointC, pointD, false, false);
+ exporter.fillTriangle(colix, pointA, pointB, pointC, false);
+ exporter.fillTriangle(colix, pointA, pointC, pointD, false);
}
@Override
@@ -737,12 +731,6 @@
exporter.drawSurface(meshSurface, colix);
}
-// @Override
-// public short[] getBgColixes(short[] bgcolixes) {
-// // 3D exporters cannot do background labels
-// return exporter.exportType == GData.EXPORT_CARTESIAN ? null : bgcolixes;
-// }
-
@Override
public void fillEllipsoid(P3 center, P3[] points, int x, int y, int z,
int diameter, M3 mToEllipsoidal, double[] coef,
Modified: trunk/Jmol/src/org/jmol/export/_PovrayExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2015-04-30 03:09:00 UTC
(rev 20464)
+++ trunk/Jmol/src/org/jmol/export/_PovrayExporter.java 2015-04-30 13:17:17 UTC
(rev 20465)
@@ -44,10 +44,23 @@
* Jmol 11.3.30
* Oct 2008
*
+ * Note added by Bob Hanson 4/30/2015
+ *
+ * Previously we were just writing the exact perspective scene from Jmol
+ * using an orthographic camera. However, the problem with z not being linear
+ * in this mode caused both Jmol and POV-Ray to incorrectly place the z value
+ * of pixels, which was particularly noticeable for large triangles.
+ * (See org.jmol.g3d/PrecisionRenderer.java)
+ *
+ * The solution is to temporarily set the Jmol renderer to orthographic mode
after
+ * getting the needed constants.
+ *
*/
public class _PovrayExporter extends __RayTracerExporter {
+ private String perspective;
+
public _PovrayExporter() {
commentChar = "// ";
}
@@ -60,6 +73,7 @@
@Override
protected void outputHeader() {
+ perspective = getJmolPerspective();
initVars();
output("// ******************************************************\n");
output("// Created by Jmol " + Viewer.getJmolVersion() + "\n");
@@ -67,11 +81,13 @@
output("// This script was generated on " + getExportDate() + "\n");
output("// ******************************************************\n");
try {
- output(vwr.getWrappedStateScript());
+ output(vwr.getWrappedStateScript());
} catch (Exception e) {
// tough luck
}
output("\n");
+ output(perspective);
+ output("\n");
output("// ******************************************************\n");
output("// Declare the resolution, camera, and light sources.\n");
output("// ******************************************************\n");
@@ -86,29 +102,39 @@
output("#declare showBonds = true;\n");
output("#declare noShadows = true;\n");
output("camera{\n");
- output(" orthographic\n");
- output(" location < " + screenWidth / 2f + ", " + screenHeight / 2f
- + ", 0>\n" + "\n");
- output(" // Negative right for a right hand coordinate system.\n");
- output("\n");
+ float offsetX, offsetY, f;
+ if (wasPerspective) {
+ offsetX = vwr.tm.getTranslationXPercent() / 100 * screenWidth;
+ offsetY = vwr.tm.getTranslationYPercent() / 100 * screenHeight;
+ f = 1f/vwr.tm.getPerspectiveFactor(2500);
+ output(" perspective\n");
+ output(" angle " + aperatureAngle + "\n");
+ output(" right < " + screenWidth + ", 0, 0>\n");
+ output(" up < 0, " + -screenHeight + ", 0 >\n");
+ } else {
+ offsetX = offsetY = f = 0;
+ output(" orthographic\n");
+ output(" right < " + -screenWidth + ", 0, 0>\n");
+ output(" up < 0, " + screenHeight + ", 0 >\n");
+ }
output(" sky < 0, -1, 0 >\n");
- output(" right < -" + screenWidth + ", 0, 0>\n");
- output(" up < 0, " + screenHeight + ", 0 >\n");
- output(" look_at < " + screenWidth / 2f + ", " + screenHeight / 2f
+ output(" location < " + (screenWidth / 2f + offsetX) + ", " +
(screenHeight / 2f + offsetY)
+ + ", 0>\n");
+ output(" look_at < " + (screenWidth / 2f + f * offsetX) + ", " +
(screenHeight / 2f + f * offsetY)
+ ", 1000 >\n");
output("}\n");
output("\n");
- output("background { color rgb <" +
- rgbFractionalFromColix(backgroundColix)
+ output("background { color rgb <" + rgbFractionalFromColix(backgroundColix)
+ "> }\n");
output("\n");
// light source
float distance = Math.max(screenWidth, screenHeight);
- output("light_source { <" + lightSource.x * distance + "," + lightSource.y
* distance
- + ", " + (-1 * lightSource.z * distance) + "> " + " rgb <0.6,0.6,0.6>
}\n");
+ output("light_source { <" + lightSource.x * distance + "," + lightSource.y
+ * distance + ", " + (-1 * lightSource.z * distance) + "> "
+ + " rgb <0.6,0.6,0.6> }\n");
output("\n");
output("\n");
Modified: trunk/Jmol/src/org/jmol/export/_TachyonExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_TachyonExporter.java 2015-04-30
03:09:00 UTC (rev 20464)
+++ trunk/Jmol/src/org/jmol/export/_TachyonExporter.java 2015-04-30
13:17:17 UTC (rev 20465)
@@ -48,7 +48,6 @@
public class _TachyonExporter extends __RayTracerExporter {
- boolean wasPerspectiveDepth;
String lighting;
String phong;
@@ -60,8 +59,6 @@
@Override
boolean initializeOutput(Viewer vwr, double privateKey, GData gdata,
Map<String, Object> params) {
- //wasPerspectiveDepth = vwr.getPerspectiveDepth();
- //vwr.setPerspectiveDepth(false);
getLightingInfo();
return initOutput(vwr, privateKey, gdata, params);
}
Modified: trunk/Jmol/src/org/jmol/export/__CartesianExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/__CartesianExporter.java 2015-04-30
03:09:00 UTC (rev 20464)
+++ trunk/Jmol/src/org/jmol/export/__CartesianExporter.java 2015-04-30
13:17:17 UTC (rev 20465)
@@ -349,16 +349,10 @@
@Override
protected void fillTriangle(short colix, T3 ptA, T3 ptB,
- T3 ptC, boolean twoSided, boolean isCartesian) {
- if (isCartesian) {
- tempP1.setT(ptA);
- tempP2.setT(ptB);
- tempP3.setT(ptC);
- } else {
+ T3 ptC, boolean twoSided) {
tm.unTransformPoint(ptA, tempP1);
tm.unTransformPoint(ptB, tempP2);
tm.unTransformPoint(ptC, tempP3);
- }
outputTriangle(tempP1, tempP2, tempP3, colix);
if (twoSided)
outputTriangle(tempP1, tempP3, tempP2, colix);
Modified: trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java 2015-04-30
03:09:00 UTC (rev 20464)
+++ trunk/Jmol/src/org/jmol/export/__RayTracerExporter.java 2015-04-30
13:17:17 UTC (rev 20465)
@@ -26,8 +26,11 @@
package org.jmol.export;
+import java.util.Map;
+
import org.jmol.modelset.Atom;
import org.jmol.util.GData;
+import org.jmol.viewer.Viewer;
import javajs.util.M3;
import javajs.util.M4;
@@ -45,6 +48,7 @@
protected boolean isSlabEnabled;
protected int minScreenDimension;
+ protected boolean wasPerspective;
public __RayTracerExporter() {
exportType = GData.EXPORT_RAYTRACER;
@@ -52,6 +56,25 @@
}
@Override
+ protected boolean initOutput(Viewer vwr, double privateKey, GData g3d,
+ Map<String, Object> params) {
+ wasPerspective = vwr.tm.perspectiveDepth;
+ if (super.initOutput(vwr, privateKey, g3d, params)) {
+ vwr.tm.perspectiveDepth = false;
+ if (wasPerspective)
+ vwr.shm.finalizeAtoms(null, null);
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ protected String finalizeOutput2() {
+ vwr.tm.perspectiveDepth = wasPerspective;
+ return super.finalizeOutput2();
+ }
+
+ @Override
protected void outputVertex(T3 pt, T3 offset) {
setTempVertex(pt, offset, tempP1);
tm.transformPt3f(tempP1, tempP1);
@@ -196,11 +219,11 @@
@Override
void fillCylinderScreenMad(short colix, byte endcaps, int diameter,
P3 screenA, P3 screenB) {
+ if (diameter == 0)
+ return;
+ if (diameter < 1)
+ diameter = 1;
float radius = diameter / 2f;
- if (radius == 0)
- return;
- if (radius < 1)
- radius = 1;
if (screenA.distance(screenB) == 0) {
outputSphere(screenA.x, screenA.y, screenA.z, radius, colix);
return;
@@ -226,7 +249,7 @@
}
@Override
- protected void fillTriangle(short colix, T3 ptA, T3 ptB, T3 ptC, boolean
twoSided, boolean isCartesian) {
+ protected void fillTriangle(short colix, T3 ptA, T3 ptB, T3 ptC, boolean
twoSided) {
outputTriangle(ptA, ptB, ptC, colix);
}
Modified: trunk/Jmol/src/org/jmol/export/___Exporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/___Exporter.java 2015-04-30 03:09:00 UTC
(rev 20464)
+++ trunk/Jmol/src/org/jmol/export/___Exporter.java 2015-04-30 13:17:17 UTC
(rev 20465)
@@ -144,8 +144,6 @@
protected String fileName;
protected String commandLineOptions;
- public boolean isCartesian;
-
protected GData gdata;
protected short backgroundColix;
@@ -205,7 +203,7 @@
this.vwr = vwr;
tm = vwr.tm;
isWebGL = params.get("type").equals("JS");
- this.gdata = g3d;
+ gdata = g3d;
this.privateKey = privateKey;
backgroundColix = vwr.getObjectColix(StateManager.OBJ_BACKGROUND);
center.setT(tm.fixedRotationCenter);
@@ -324,6 +322,10 @@
return rgbFractionalFromArgb(gdata.getColorArgbOrGray(colix));
}
+ protected String getTriadC(T3 t) {
+ return getTriad(t);
+ }
+
protected String getTriad(T3 t) {
return round(t.x) + " " + round(t.y) + " " + round(t.z);
}
@@ -337,7 +339,7 @@
tempC.set(red == 0 ? 0 : (red + 1)/ 256f,
green == 0 ? 0 : (green + 1) / 256f,
blue == 0 ? 0 : (blue + 1) / 256f);
- return getTriad(tempC);
+ return getTriadC(tempC);
}
protected static String translucencyFractionalFromColix(short colix) {
@@ -563,7 +565,7 @@
abstract void fillSphere(short colix, int diameter, P3 pt);
//cartoons, rockets, polyhedra:
- protected abstract void fillTriangle(short colix, T3 ptA0, T3 ptB0, T3 ptC0,
boolean twoSided, boolean isCartesian);
+ protected abstract void fillTriangle(short colix, T3 ptA0, T3 ptB0, T3 ptC0,
boolean twoSided);
private int nText;
Modified: trunk/Jmol/src/org/jmol/g3d/CircleRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/CircleRenderer.java 2015-04-30 03:09:00 UTC
(rev 20464)
+++ trunk/Jmol/src/org/jmol/g3d/CircleRenderer.java 2015-04-30 13:17:17 UTC
(rev 20465)
@@ -155,13 +155,13 @@
Pixelator p = g.pixel;
while (x >= y) {
- g.plotPixelsClipped(c, 2 * x + 1 - sizeCorrection, xCenter - x, yCenter
+ plotPixelsClipped(c, 2 * x + 1 - sizeCorrection, xCenter - x, yCenter
+ y - sizeCorrection, zCenter, width, height, zbuf, p);
- g.plotPixelsClipped(c, 2 * x + 1 - sizeCorrection, xCenter - x, yCenter
+ plotPixelsClipped(c, 2 * x + 1 - sizeCorrection, xCenter - x, yCenter
- y, zCenter, width, height, zbuf, p);
- g.plotPixelsClipped(c, 2 * y + 1 - sizeCorrection, xCenter - y, yCenter
+ plotPixelsClipped(c, 2 * y + 1 - sizeCorrection, xCenter - y, yCenter
+ x - sizeCorrection, zCenter, width, height, zbuf, p);
- g.plotPixelsClipped(c, 2 * y + 1 - sizeCorrection, xCenter - y, yCenter
+ plotPixelsClipped(c, 2 * y + 1 - sizeCorrection, xCenter - y, yCenter
- x, zCenter, width, height, zbuf, p);
++y;
radiusError += yChange;
@@ -174,6 +174,29 @@
}
}
+ private void plotPixelsClipped(int argb, int count, int x, int y, int z, int
width,
+ int height, int[] zbuf, Pixelator p) {
+ // for circle only; i.e. halo
+ // simple Z/window clip
+ if (y < 0 || y >= height || x >= width)
+ return;
+ if (x < 0) {
+ count += x; // x is negative, so this is subtracting -x
+ x = 0;
+ }
+ if (count + x > width)
+ count = width - x;
+ if (count <= 0)
+ return;
+ int offsetPbuf = y * width + x;
+ int offsetMax = offsetPbuf + count;
+ while (offsetPbuf < offsetMax) {
+ if (z < zbuf[offsetPbuf])
+ p.addPixel(offsetPbuf, z, argb);
+ offsetPbuf++;// += step;
+ }
+ }
+
void plotFilledCircleCenteredUnclipped(int xCenter, int yCenter, int zCenter,
int diameter) {
// for halo only
Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2015-04-30 03:09:00 UTC (rev
20464)
+++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java 2015-04-30 13:17:17 UTC (rev
20465)
@@ -1610,29 +1610,6 @@
}
}
- void plotPixelsClipped(int argb, int count, int x, int y, int z, int width,
- int height, int[] zbuf, Pixelator p) {
- // for circle only; i.e. halo
- // simple Z/window clip
- if (y < 0 || y >= height || x >= width)
- return;
- if (x < 0) {
- count += x; // x is negative, so this is subtracting -x
- x = 0;
- }
- if (count + x > width)
- count = width - x;
- if (count <= 0)
- return;
- int offsetPbuf = y * width + x;
- int offsetMax = offsetPbuf + count;
- while (offsetPbuf < offsetMax) {
- if (z < zbuf[offsetPbuf])
- p.addPixel(offsetPbuf, z, argb);
- offsetPbuf++;// += step;
- }
- }
-
void plotPixelsClippedRaster(int count, int x, int y, int zAtLeft,
int zPastRight, Rgb16 rgb16Left, Rgb16
rgb16Right) {
// cylinder3d.renderFlatEndcap, triangle3d.fillRaster
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-04-30 03:09:00 UTC
(rev 20464)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-04-30 13:17:17 UTC
(rev 20465)
@@ -14,9 +14,12 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
+Jmol.___JmolVersion="14.3.13_2015.04.30"
-Jmol.___JmolVersion="14.3.13_2015.04.29"
+bug fix: POV-Ray fixed for perspective and orthographic cameras using new
z-depth formula.
+JmolVersion="14.3.13_2015.04.29"
+
bug fix: perspective renderer was using the wrong formula for calculating Z
depth of pixels:
* Note added 4/2015 BH:
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-04-30
03:09:00 UTC (rev 20464)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-04-30
13:17:17 UTC (rev 20465)
@@ -1149,7 +1149,6 @@
* This method returns data needed by the VRML, X3D, and IDTF/U3D exporters.
* It also should serve as a valuable resource for anyone adapting Jmol and
* wanting to know how the Jmol 11+ camera business works.
- *
* @return a set of camera data
*/
public P3[] getCameraFactors() {
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