Thread: [Jmol-commits] SF.net SVN: jmol:[14005] branches/v12_0/Jmol/src/org/jmol (Page 2)

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Revision: 14005
          http://jmol.svn.sourceforge.net/jmol/?rev=14005&view=rev
Author:   hansonr
Date:     2010-08-16 17:01:26 +0000 (Mon, 16 Aug 2010)

Log Message:
-----------
version=12.0.7_dev

# bug fix: isosurface colorscheme TRANSLUCENT "xxx" fillTriangle error
# bug fix: should not allow isosurface ... map colorscheme "xxx" TRANSLUCENT

Modified Paths:
--------------
    branches/v12_0/Jmol/src/org/jmol/g3d/Graphics3D.java
    branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
    branches/v12_0/Jmol/src/org/jmol/shapesurface/Isosurface.java
    branches/v12_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
    branches/v12_0/Jmol/src/org/jmol/util/ColorEncoder.java
    branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties

Modified: branches/v12_0/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================

--- branches/v12_0/Jmol/src/org/jmol/g3d/Graphics3D.java	2010-08-16 16:48:09 UTC (rev 14004)
+++ branches/v12_0/Jmol/src/org/jmol/g3d/Graphics3D.java	2010-08-16 17:01:26 UTC (rev 14005)
@@ -214,7 +214,6 @@
   short colixCurrent;
   int[] shadesCurrent;
   int argbCurrent;
-  boolean isTranslucent;
   boolean isScreened;
   int translucencyMask;
   int argbNoisyUp, argbNoisyDn;
@@ -708,15 +707,6 @@
 
   private int currentShadeIndex;
   
-  private void setColixAndShadeIndex(short colix, int shadeIndex) {
-    if (colix == colixCurrent && currentShadeIndex == shadeIndex)
-      return;
-    currentShadeIndex = -1;
-    setColix(colix);
-    setColorNoisy(shadeIndex);
-  }
-
-  
   /**
    * sets current color from colix color index
    * @param colix the color index
@@ -728,7 +718,7 @@
     int mask = colix & TRANSLUCENT_MASK;
     if (mask == TRANSPARENT)
       return false;
-    isTranslucent = mask != 0;
+    boolean isTranslucent = mask != 0;
     isScreened = isTranslucent && mask == TRANSLUCENT_SCREENED;
     if (!checkTranslucent(isTranslucent && !isScreened))
       return false;
@@ -1330,32 +1320,6 @@
     triangle3d.fillTriangle(xA, yA, zA, xB, yB, zB, xC, yC, zC, false);
   }
   */
-  public void fillTriangle(Point3i screenA, short colixA, short normixA,
-                           Point3i screenB, short colixB, short normixB,
-                           Point3i screenC, short colixC, short normixC) {
-    // mesh, isosurface
-    boolean useGouraud;
-    if (normixA == normixB && normixA == normixC &&
-        colixA == colixB && colixA == colixC) {
-      setColixAndShadeIndex(colixA, normix3d.getShadeIndex(normixA));
-      useGouraud = false;
-    } else {
-      triangle3d.setGouraud(getShades(colixA)[normix3d.getShadeIndex(normixA)],
-                            getShades(colixB)[normix3d.getShadeIndex(normixB)],
-                            getShades(colixC)[normix3d.getShadeIndex(normixC)]);
-      int translucentCount = 0;
-      if (isColixTranslucent(colixA))
-        ++translucentCount;
-      if (isColixTranslucent(colixB))
-        ++translucentCount;
-      if (isColixTranslucent(colixC))
-        ++translucentCount;
-      isTranslucent = translucentCount >= 2;
-      useGouraud = true;
-    }
-    triangle3d.fillTriangle(screenA, screenB, screenC, useGouraud);
-  }
-
   public void fillTriangleTwoSided(short normix,
                            int xScreenA, int yScreenA, int zScreenA,
                            int xScreenB, int yScreenB, int zScreenB,
@@ -1378,35 +1342,73 @@
     triangle3d.fillTriangle(screenA, screenB, screenC, false);
   }
 
-  public void fillTriangle(Point3i screenA, short colixA,
-                                   short normixA, Point3i screenB,
-                                   short colixB, short normixB,
-                                   Point3i screenC, short colixC,
-                                   short normixC, float factor) {
+  public void fillTriangle(Point3i screenA, short colixA, short normixA,
+                           Point3i screenB, short colixB, short normixB,
+                           Point3i screenC, short colixC, short normixC,
+                           float factor) {
     // isosurface test showing triangles
     boolean useGouraud;
-    if (normixA == normixB && normixA == normixC && colixA == colixB
-        && colixA == colixC) {
-      setColixAndShadeIndex(colixA, normix3d.getShadeIndex(normixA));
+    if (!isPass2 && normixA == normixB && normixA == normixC
+        && colixA == colixB && colixA == colixC) {
+      setTriangleColixAndShadeIndex(colixA, normix3d.getShadeIndex(normixA));
       useGouraud = false;
     } else {
+      if (!setTriangleTranslucency(colixA, colixB, colixC))
+        return;
       triangle3d.setGouraud(getShades(colixA)[normix3d.getShadeIndex(normixA)],
           getShades(colixB)[normix3d.getShadeIndex(normixB)],
           getShades(colixC)[normix3d.getShadeIndex(normixC)]);
-      int translucentCount = 0;
-      if (isColixTranslucent(colixA))
-        ++translucentCount;
-      if (isColixTranslucent(colixB))
-        ++translucentCount;
-      if (isColixTranslucent(colixC))
-        ++translucentCount;
-      isTranslucent = translucentCount >= 2;
       useGouraud = true;
     }
-    triangle3d.fillTriangle(screenA, screenB, screenC, factor,
-        useGouraud);
+    triangle3d.fillTriangle(screenA, screenB, screenC, factor, useGouraud);
   }
 
+  public void fillTriangle(Point3i screenA, short colixA, short normixA,
+                           Point3i screenB, short colixB, short normixB,
+                           Point3i screenC, short colixC, short normixC) {
+    // mesh, isosurface
+    boolean useGouraud;
+    if (!isPass2 && normixA == normixB && normixA == normixC
+        && colixA == colixB && colixA == colixC) {
+      setTriangleColixAndShadeIndex(colixA, normix3d.getShadeIndex(normixA));
+      useGouraud = false;
+    } else {
+      if (!setTriangleTranslucency(colixA, colixB, colixC))
+        return;
+      triangle3d.setGouraud(getShades(colixA)[normix3d.getShadeIndex(normixA)],
+          getShades(colixB)[normix3d.getShadeIndex(normixB)],
+          getShades(colixC)[normix3d.getShadeIndex(normixC)]);
+      useGouraud = true;
+    }
+    triangle3d.fillTriangle(screenA, screenB, screenC, useGouraud);
+  }
+
+  private void setTriangleColixAndShadeIndex(short colix, int shadeIndex) {
+    if (colix == colixCurrent && currentShadeIndex == shadeIndex)
+      return;
+    currentShadeIndex = -1;
+    setColix(colix);
+    setColorNoisy(shadeIndex);
+  }
+
+  private boolean setTriangleTranslucency(short colixA, short colixB,
+                                          short colixC) {
+    if (!isPass2)
+      return true;
+    int maskA = colixA & TRANSLUCENT_MASK;
+    int maskB = colixB & TRANSLUCENT_MASK;
+    int maskC = colixC & TRANSLUCENT_MASK;
+    maskA &= ~TRANSPARENT;
+    maskB &= ~TRANSPARENT;
+    maskC &= ~TRANSPARENT;
+    //if (maskA == 0 && maskB == 0 && maskC == 0)
+    //return false;
+    int mask = ((maskA + maskB + maskC) / 3) & TRANSLUCENT_MASK;
+    // System.out.println(mask >> TRANSLUCENT_SHIFT);
+    translucencyMask = (mask << ALPHA_SHIFT) | 0xFFFFFF;
+    return true;
+  }
+
   /* ***************************************************************
    * quadrilaterals
    * ***************************************************************/

Modified: branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java	2010-08-16 16:48:09 UTC (rev 14004)
+++ branches/v12_0/Jmol/src/org/jmol/script/ScriptEvaluator.java	2010-08-16 17:01:26 UTC (rev 14005)
@@ -15254,17 +15254,13 @@
         i = iToken;
         break;
       case Token.colorscheme:
-        sbCommand.append(" colorScheme");
-        // either order OK -- documented for "rwb" TRANSLUCENT
+        // either order NOT OK -- documented for TRANSLUCENT "rwb" 
         if (tokAt(i + 1) == Token.translucent) {
           isColorSchemeTranslucent = true;
           i++;
         }
         colorScheme = parameterAsString(++i);
-        if (tokAt(i + 1) == Token.translucent) {
-          isColorSchemeTranslucent = true;
-          i++;
-        }
+        sbCommand.append(" colorScheme");
         if (isColorSchemeTranslucent)
           sbCommand.append(" translucent");
         sbCommand.append(" ").append(Escape.escape(colorScheme));

Modified: branches/v12_0/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- branches/v12_0/Jmol/src/org/jmol/shapesurface/Isosurface.java	2010-08-16 16:48:09 UTC (rev 14004)
+++ branches/v12_0/Jmol/src/org/jmol/shapesurface/Isosurface.java	2010-08-16 17:01:26 UTC (rev 14005)
@@ -480,7 +480,8 @@
 
     if ("setColorScheme" == propertyName) {
       String schemeName = ((String) ((Object[]) value)[0]);
-      setColorCommand(schemeName, true);
+      boolean isTranslucent = ((Boolean)((Object[]) value)[1]).booleanValue();
+      setColorCommand(schemeName, isTranslucent, true);
       return;
     }
 
@@ -950,6 +951,7 @@
   public void notifySurfaceMappingCompleted() {
     setModelIndex();
     String schemeName = colorEncoder.getColorSchemeName();
+    boolean isTranslucentScheme = colorEncoder.isTranslucent();
     viewer.setPropertyColorScheme(schemeName, sg.getParams().colorSchemeTranslucent, false);
     viewer.setCurrentColorRange(jvxlData.valueMappedToRed,
         jvxlData.valueMappedToBlue);
@@ -965,7 +967,7 @@
     setPropertySuper("token", new Integer(explicitContours ? Token.nofill : Token.fill), null);
     setPropertySuper("token", new Integer(explicitContours ? Token.contourlines : Token.nocontourlines), null);
     // may not be the final color scheme, though.
-    setColorCommand(schemeName, true);
+    setColorCommand(schemeName, isTranslucentScheme, true);
     /*
      viewer.setCurrentColorRange(jvxlData.mappedDataMin, jvxlData.mappedDataMax);
      thisMesh.isColorSolid = false;
@@ -976,11 +978,13 @@
      */
   }
 
-  private void setColorCommand(String schemeName, boolean useJvxlData) {
+  private void setColorCommand(String schemeName, boolean isTranslucent, boolean useJvxlData) {
     if (thisMesh == null)
       return;
-    thisMesh.colorCommand = "color $" + thisMesh.thisID + " "
-        + getUserColorScheme(schemeName) + " range ";
+    String colors = viewer.getColorSchemeList(schemeName, false);
+    thisMesh.colorCommand = "color $" + thisMesh.thisID 
+        + (isTranslucent ? " translucent " : " ") + Escape.escape(
+        colors.length() == 0 ? schemeName : colors) + " range ";
     if (useJvxlData) {
       thisMesh.colorCommand += (jvxlData.isColorReversed ? jvxlData.valueMappedToBlue
           + " " + jvxlData.valueMappedToRed
@@ -1112,9 +1116,15 @@
       vertexColixes = thisMesh.vertexColixes = new short[thisMesh.vertexCount];
     boolean isTranslucent = Graphics3D.isColixTranslucent(thisMesh.colix)
      && !Graphics3D.isColixTranslucent(viewer.getColixForPropertyValue(Float.NaN));
+    boolean isTranslucentScheme = false;
+    String scheme = viewer.getPropertyColorScheme();
+    if (scheme.startsWith("translucent ")) {
+      isTranslucentScheme = true;
+      scheme = scheme.substring(12).trim();
+    }
     for (int i = thisMesh.vertexCount; --i >= 0;) {
       vertexColixes[i] = viewer.getColixForPropertyValue(vertexValues[i]);
-      if (isTranslucent)
+      if (isTranslucent && !isTranslucentScheme)
         vertexColixes[i] = Graphics3D.getColixTranslucent(vertexColixes[i], true, translucentLevel);
     }
     Vector[] contours = thisMesh.getContours();
@@ -1140,15 +1150,10 @@
     jvxlData.valueMappedToBlue = Math.max(range[0], range[1]);
     jvxlData.isJvxlPrecisionColor = true;
     JvxlCoder.jvxlCreateColorData(jvxlData, vertexValues);
-    setColorCommand(viewer.getPropertyColorScheme(), false);
+    setColorCommand(scheme, isTranslucentScheme, false);
     thisMesh.isColorSolid = false;
   }
 
-  private String getUserColorScheme(String schemeName) {
-    String colors = viewer.getColorSchemeList(schemeName, false);
-    return "\"" + (colors.length() == 0 ? schemeName : colors) + "\"";
-  }
-  
   public void getPlane(int x) {
     // only for surface readers
   }

Modified: branches/v12_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java
===================================================================
--- branches/v12_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java	2010-08-16 16:48:09 UTC (rev 14004)
+++ branches/v12_0/Jmol/src/org/jmol/shapesurface/IsosurfaceRenderer.java	2010-08-16 17:01:26 UTC (rev 14005)
@@ -257,7 +257,7 @@
         if (transformedVectors[nC].z < 0)
           check ^= 4;
       }
-      if (fill && check != 7)
+      if (fill && check == 0)
         continue;
       short colixA, colixB, colixC;
       if (colorSolid) {

Modified: branches/v12_0/Jmol/src/org/jmol/util/ColorEncoder.java
===================================================================
--- branches/v12_0/Jmol/src/org/jmol/util/ColorEncoder.java	2010-08-16 16:48:09 UTC (rev 14004)
+++ branches/v12_0/Jmol/src/org/jmol/util/ColorEncoder.java	2010-08-16 17:01:26 UTC (rev 14005)
@@ -194,6 +194,10 @@
   public String getColorSchemeName() {
     return getColorSchemeName(currentPalette);  
   }
+
+  public boolean isTranslucent() {
+    return currentTranslucent;
+  }
   
   public final static String getColorSchemeName(int i) {
     int absi = Math.abs(i);

Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties	2010-08-16 16:48:09 UTC (rev 14004)
+++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties	2010-08-16 17:01:26 UTC (rev 14005)
@@ -4,6 +4,8 @@
 
 version=12.0.7_dev
 
+# bug fix: isosurface colorscheme TRANSLUCENT "xxx" fillTriangle error
+# bug fix: should not allow isosurface ... map colorscheme "xxx" TRANSLUCENT
 # bug fix: CRYSTAL reader FREQUENCY when input deck is missing VIBRATION record
 
 # --------------------------------------------------------------


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Thread: [Jmol-commits] SF.net SVN: jmol:[14005] branches/v12_0/Jmol/src/org/jmol (Page 2)

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