MO Compute: build the isosurface at the requested cutoff (#226)

IsoSurfaceCmd built every surface at a hard-wired 0.05 (0.002 for ESP)
and MoPanel applied the slider's cutoff afterwards with IsoValueCmd. Each
Builder::execute() ends in a synchronous paint (refreshRenderArea is
Refresh + Update), so the 0.05 surface was drawn twice, after
IsoSurfaceCmd and after SurfDisplayTypeCmd, before the requested one.

IsoSurfaceCmd takes an "isovalue" parameter (0 keeps the field-type
default, so other callers are unchanged); MoPanel computes the initial
cutoff first and passes it, and the ESP colour-range rebuild passes the
slider's. The ESP colour shell still uses the default cutoff, as before.

Verified with tools/coin/scenes/calc-water-mopanel.scene on
calc-water-vib (HOMO): before, frames 4-5 carry thresholds +/-0.05 and
ChemIso generates at 0.05 then 0.150818; after, every frame carries
+/-0.150818 and only that surface is generated. Final frame
pixel-identical before and after.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PFPK14wBcLD1s4dYUowpP4

Author: andy

docs/claude/wx-viewer/builder-execute-paints-after-every-command.md

@@ -0,0 +1,24 @@
+---
+type: pitfall
+title: "`Builder::execute()` paints after every command, so a command sequence shows each intermediate state (#226)"
+area: wx-viewer
+paths: [src/apps/builder/Builder.C, src/wxviz/viewer/SGViewer.C, src/apps/builder/MoPanel.C, src/viz/propsgcommands/IsoSurfaceCmd.C, src/viz/propsgcommands/IsoValueCmd.C, src/inv/moiv/ChemIso.C]
+issues: [226]
+---
+`Builder::execute(cmd)` (non-batch) ends with `SGViewer::refreshRenderArea()`,
+which is `Refresh(false)` + `Update()`: a synchronous paint. A panel that
+reaches its final scene through several commands therefore puts every
+intermediate scene on screen, one frame each.
+
+MoPanel's Compute ran `IsoSurfaceCmd` (built at a hard-wired 0.05, 0.002
+for ESP), `SurfDisplayTypeCmd`, then `IsoValueCmd` (the slider's cutoff):
+two frames of a 0.05 surface before the requested one. `IsoSurfaceCmd` now
+takes an `isovalue` parameter (0 = the field-type default) and MoPanel
+passes the cutoff it is about to put on the slider. Cube.C still builds at
+the default and never applies its slider on grid selection.
+
+To see it headlessly: `tools/coin/scenes/calc-water-mopanel.scene`
+(`mopanel <name>`, a Builder-only scene command) presses Compute and writes
+every frame of the Builder canvas with the thresholds of the `ChemIso`
+nodes in the scene at that frame; `ECCE_DEBUG_ISO=1` also logs each surface
+`ChemIso::regenerate` actually generates.

docs/claude/wx-viewer/index.md

@@ -15,6 +15,8 @@ Read this before changing any dialog, panel, sizer, grid, ewx control or the Ope
 - [`ECCE_USE_COIN` (default ON) builds the viewer against Coin3D; `=OFF` keeps the vendored core for one release](ecce-use-coin-builds-the-viewer-against-coin3d.md)
 - [Coin SORTED_LAYERS_BLEND is the default lobe transparency (6 passes, alpha canvas); slow scenes fall back to SCREEN_DOOR](coin-sorted-layers-blend-is-the-default-lobe-transparency.md)
 - [`GlPlatform` is the viewer's only GLX/EGL code; `tools/nonx11/check.py` compiles the viewer as a non-X11 port (#232)](glplatform-is-the-viewers-only-glx-egl-code.md)
+- [`Builder::execute()` paints after every command, so a command sequence shows each intermediate state (#226)](builder-execute-paints-after-every-command.md)
+- [Normal-mode arrows start at the atom centre and scale uniformly; small ones end inside the sphere (#228)](normal-mode-arrows-start-at-the-atom-centre.md)
 - [`tools/coin/compare.sh` renders a fixed scene set with both viewer builds (#166 stage 2); harness pitfalls](tools-coin-compare-sh-renders-both-viewer-builds.md)
 - [Atom labels drew nothing in 9.x: the sh wrappers dropped `FL_FONT_PATH`; flclient now defaults to `$ECCE_HOME/data/client/fonts`](atom-labels-need-the-bundled-font-fl-font-path.md)
 - [Builder Reset View (toolbar, Render menu, Home) is camera only; the old home button restored a pre-molecule camera](builder-reset-view-is-camera-only-home-key.md)

src/apps/builder/MoPanel.C

@@ -981,20 +981,6 @@ void MoPanel::OnButtonMoComputeClick( wxCommandEvent& event )
       double posR, posG, posB, negR, negG, negB;
       getSurfaceColors(posR, posG, posB, negR, negG, negB);
 
-      cmd = new IsoSurfaceCmd("Iso Surface", &sg, expt);
-      applyEspRange(cmd);
-      cmd->getParameter("transparency")->setDouble(getTransparency());
-      cmd->getParameter("positiveRed")->setDouble(posR);
-      cmd->getParameter("positiveGreen")->setDouble(posG);
-      cmd->getParameter("positiveBlue")->setDouble(posB);
-      cmd->getParameter("negativeRed")->setDouble(negR);
-      cmd->getParameter("negativeGreen")->setDouble(negG);
-      cmd->getParameter("negativeBlue")->setDouble(negB);
-      fw.execute(cmd);
-
-      updateSurface();
-
-
       // Determine max abs value of field for the (abs value) slider
       // Bruce says that for spin density, its better to hardwire the max
       // scale to no omre than 1.0 but probably even less.
@@ -1035,6 +1021,22 @@ void MoPanel::OnButtonMoComputeClick( wxCommandEvent& event )
       if (espSurface) {
          isovalue = log10(0.002);
       }
+
+      cmd = new IsoSurfaceCmd("Iso Surface", &sg, expt);
+      applyEspRange(cmd);
+      cmd->getParameter("isovalue")->setDouble(pow(10.0, isovalue));
+      cmd->getParameter("transparency")->setDouble(getTransparency());
+      cmd->getParameter("positiveRed")->setDouble(posR);
+      cmd->getParameter("positiveGreen")->setDouble(posG);
+      cmd->getParameter("positiveBlue")->setDouble(posB);
+      cmd->getParameter("negativeRed")->setDouble(negR);
+      cmd->getParameter("negativeGreen")->setDouble(negG);
+      cmd->getParameter("negativeBlue")->setDouble(negB);
+      fw.execute(cmd);
+
+      updateSurface();
+
+
       p_slider->SetValue(isovalue);
       updateIsoValue(isovalue);
 
@@ -1614,6 +1616,8 @@ void MoPanel::rebuildEspSurface()
 
    Command *cmd = new IsoSurfaceCmd("Iso Surface", &sg, expt);
    applyEspRange(cmd);
+   cmd->getParameter("isovalue")->setDouble(
+         pow(10.0, static_cast<double>(p_slider->GetFloatValue())));
    cmd->getParameter("transparency")->setDouble(getTransparency());
    cmd->getParameter("positiveRed")->setDouble(posR);
    cmd->getParameter("positiveGreen")->setDouble(posG);

src/viz/propsgcommands/IsoSurfaceCmd.C

@@ -59,6 +59,12 @@ void IsoSurfaceCmd::init()
    addParameter(new CommandParameter("colorMin", -0.05));
    addParameter(new CommandParameter("colorMax", 0.05));
 
+   //  The cutoff to build the surface at; 0 or less means the field
+   //  type's default below.  A caller that knows the user's cutoff passes
+   //  it: building at the default first showed that surface for a frame
+   //  or two before IsoValueCmd replaced it (#226).
+   addParameter(new CommandParameter("isovalue", 0.0));
+
 }
 
 bool IsoSurfaceCmd::execute()
@@ -287,8 +293,12 @@ bool IsoSurfaceCmd::execute()
         }
       }
 
+      const double requested = getParameter("isovalue")->getDouble();
+      const float threshold = requested > 0.0 ? (float)requested : isovalue;
+      ISO_LOG << "ISO: building at threshold " << threshold << std::endl;
+
       // Since we only deal with absolute values of isovalues:
-      if (isovalue > 0.0) {
+      if (threshold > 0.0) {
          positiveLobeColor = posColor;
          negativeLobeColor = negColor;
       }
@@ -331,7 +341,7 @@ bool IsoSurfaceCmd::execute()
                           gridStruct->colorFieldMax(), transparency);
       }
 
-      isosurf1->threshold.setValue(isovalue);
+      isosurf1->threshold.setValue(threshold);
 
 #ifndef MI10
       /* Well, I guess I sort of screwed you over here, but nothing that can't be
@@ -378,7 +388,7 @@ bool IsoSurfaceCmd::execute()
 
          isosurf2->dataVar = 0;
          isosurf2->colorVar = 0;
-         isosurf2->threshold.setValue(-isovalue);
+         isosurf2->threshold.setValue(-threshold);
 
 #ifndef MI10
          childList = isosurf2->getChildren();
@@ -410,13 +420,13 @@ bool IsoSurfaceCmd::execute()
       chemMesh->kAxis.setValue(true);
       chemMesh->dataVar = 0;
 
-      chemMesh->levels.set1Value(0, isovalue);
+      chemMesh->levels.set1Value(0, threshold);
       chemMesh->orderedRGBA.set1Value(0, positiveLobeColor);
 
       // For other than Density field, we want to display both positive and
       // negative lobes (isosurfaces)
       if (!densityLike) {
-         chemMesh->levels.set1Value(1, -isovalue);
+         chemMesh->levels.set1Value(1, -threshold);
          chemMesh->orderedRGBA.set1Value(1, negativeLobeColor);
       }
 
@@ -438,15 +448,15 @@ bool IsoSurfaceCmd::execute()
       chemContour->kAxis.setValue(false);
       chemContour->dataVar = 0;
 
-      chemContour->levels.set1Value(0, isovalue);
+      chemContour->levels.set1Value(0, threshold);
       chemContour->orderedRGBA.set1Value(0, positiveLobeColor);
       //  vp = (SoVertexProperty *)chemContour->vertexProperty.getValue();
       //  vp->orderedRGBA.setValue(positiveLobeColor);
 
       // For other than Density field, we want to display both positive and
       // negative lobes (isosurfaces)
       if (!densityLike) {
-         chemContour->levels.set1Value(1, -isovalue);
+         chemContour->levels.set1Value(1, -threshold);
          chemContour->orderedRGBA.set1Value(1, negativeLobeColor);
       }