Rugnux: warn about further lattices only where they are domains of the crystal

MULTIPLE_LATTICES and EXTRA_LATTICE_INTENSITY_PCT now count DOMAIN, TWIN_DOMAIN and SEGMENTED
lattices only. A FOREIGN lattice (an unrelated cell) is still listed but no longer warned about: it
is as often a wrong main lattice or tNCS as a second crystal (one of the four such sets in the
battery census is a tNCS crystal). On the census this names 25 of 200 rotation sets instead of 29.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C

docs/CHANGELOG.md

@@ -23,7 +23,7 @@
 * Rugnux puts the merge onto a reference MTZ's axes before inheriting its free-R flags, and does not inherit them where the merge does not match the reference (`REFERENCE_MISMATCH`); `REFERENCE_OPERATOR=`, `REFERENCE_CC=` and `REFERENCE_MATCHED_FRACTION=` report the match.
 * Rugnux places a space group given with `-S` on the axes its systematic absences name, so `-S 18` on a cell whose pure two-fold is not its longest axis no longer merges with the screw absences on the wrong rows.
 * `rugnux -z` also takes a PDB structure-factor mmCIF (`-sf.cif`, gzipped or not) as the reference, with its R-free set; `--reference` is a new name for `--reference-mtz`.
-* Rugnux reports further lattices found in the spots the main lattice leaves over on rotation data - split-crystal and twin domains, a crystal that changes along the sweep, a related or an unrelated cell (`EXTRA_LATTICE_*` keys, a `Multiple lattices` summary line) - and warns (`MULTIPLE_LATTICES`) where they hold at least 10 % of the spot intensity; processing is unchanged.
+* Rugnux reports further lattices found in the spots the main lattice leaves over on rotation data - split-crystal and twin domains, a crystal that changes along the sweep, a related or an unrelated cell (`EXTRA_LATTICE_*` keys, a `Multiple lattices` summary line) - and warns (`MULTIPLE_LATTICES`) where domains of the crystal hold at least 10 % of the spot intensity; processing is unchanged.
 * Rugnux reports the mosaicity the merge used (`MOSAICITY_DEG=` with `MOSAICITY_DEG_P10=`/`_P90=` over the frames, and a summary line), as XDS's sigma_M (`REFLECTING_RANGE_E.S.D.`).
 * `rugnux --polarization` is documented as the polarization degree (XDS `FRACTION_OF_POLARIZATION` = (1 + p)/2); the default 0.99 suits undulators.
 

docs/RUGNUX_REPORT.md

@@ -484,7 +484,9 @@ lattices listed. For each, numbered from 1 in the order found:
 - **`EXTRA_LATTICE_<n>_SWEEP_CONCENTRATION=`** — the share of its spots in the 2 densest of 8 blocks of the
   sweep; 0.25 is uniform.
 
-**`EXTRA_LATTICE_INTENSITY_PCT=`** sums the intensity share of every listed lattice except `RELATED_CELL`,
+**`EXTRA_LATTICE_INTENSITY_PCT=`** sums the intensity share of the domains (`DOMAIN`, `TWIN_DOMAIN`, `SEGMENTED`);
+a `RELATED_CELL` or `FOREIGN` lattice is listed but not counted, since it is as often a wrong main lattice or tNCS
+as a second crystal,
 and **`MULTIPLE_LATTICES=`** is `TRUE`, with a warning under the `MULTIPLE_LATTICES` flag, where that is
 at least 10 %. It is information, not a failure: a split crystal whose second domain is half as strong
 as the main one can still give data as good as XDS's, since the domains' reflections are only a problem

rugnux/ResultReport.cpp

@@ -59,20 +59,22 @@ namespace {
         return sc.i_over_sigma >= 0.5 && sc.rock_pct >= 2.0 && sc.rock_pct > 3.0 * sc.rock_se_pct;
     }
 
-    // A misoriented domain, a twin domain, a segment of the sweep or an unrelated crystal that together
-    // hold at least this share of the non-ice spot intensity is worth the user's look. A related cell
-    // is a question about the crystal's own cell and is left to the supercell keys. On 200 battery
-    // rotation sets this names 29: 25 with split-crystal or twin domains and 4 with an unrelated cell.
+    // Domains of the crystal itself - misoriented, turned by 180 deg, or holding a segment of the sweep -
+    // that together hold at least this share of the non-ice spot intensity are worth the user's look. A
+    // related cell is a question about the crystal's own cell (left to the supercell keys), and an
+    // unrelated cell is as often a wrong main lattice or tNCS as a second crystal: both are listed, not
+    // warned about. On 200 battery rotation sets this names 25.
     constexpr double MULTIPLE_LATTICES_INTENSITY_PCT = 10.0;
 
-    bool CountsAsSecondCrystal(const LeftoverLattice &l) {
-        return l.kind != LeftoverLatticeKind::Self && l.kind != LeftoverLatticeKind::RelatedCell;
+    bool CountsAsDomain(const LeftoverLattice &l) {
+        return l.kind == LeftoverLatticeKind::Domain || l.kind == LeftoverLatticeKind::TwinDomain
+               || l.kind == LeftoverLatticeKind::Segmented;
     }
 
-    double SecondCrystalIntensityPct(const LeftoverLatticeCensus &c) {
+    double DomainIntensityPct(const LeftoverLatticeCensus &c) {
         double pct = 0.0;
         for (const auto &l : c.lattices)
-            if (CountsAsSecondCrystal(l))
+            if (CountsAsDomain(l))
                 pct += l.intensity_pct;
         return pct;
     }
@@ -1200,17 +1202,17 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
                 Add(s, KeyReal(key("SWEEP_CONCENTRATION").c_str(), l.sweep_concentration, "{:.2f}"));
                 Add(s, KeyReal(key("Z").c_str(), l.z, "{:.1f}"));
             }
-            const double second = SecondCrystalIntensityPct(c);
+            const double second = DomainIntensityPct(c);
             const bool multiple = second >= MULTIPLE_LATTICES_INTENSITY_PCT;
             Add(s, KeyReal("EXTRA_LATTICE_INTENSITY_PCT", second, "{:.1f}"));
             Add(s, KeyBool("MULTIPLE_LATTICES", multiple));
             if (multiple) {
                 const LeftoverLattice *strongest = nullptr;
                 for (const auto &l : c.lattices)
-                    if (CountsAsSecondCrystal(l) && (!strongest || l.intensity_pct > strongest->intensity_pct))
+                    if (CountsAsDomain(l) && (!strongest || l.intensity_pct > strongest->intensity_pct))
                         strongest = &l;
                 Warn(doc, PathologyCode::MULTIPLE_LATTICES,
-                     fmt::format("Further lattices carry {:.0f}% of the spot intensity against {:.0f}% on the "
+                     fmt::format("Further domains of the crystal carry {:.0f}% of the spot intensity against {:.0f}% on the "
                                  "main one (the strongest: {}); only the main lattice is integrated. This does "
                                  "not by itself make the data worse - check the crystal, and the result",
                                  second, c.primary_intensity_pct, LeftoverLatticeLine(*strongest)));
@@ -2121,7 +2123,7 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
                                                                           c.lattices.size()) : "",
                                       LeftoverLatticeLine(*strongest), strongest->intensity_pct,
                                       c.primary_intensity_pct,
-                                      SecondCrystalIntensityPct(c) >= MULTIPLE_LATTICES_INTENSITY_PCT
+                                      DomainIntensityPct(c) >= MULTIPLE_LATTICES_INTENSITY_PCT
                                               ? " - check the crystal" : ""));
             }
             if (merged) {

tests/ResultReportTest.cpp

@@ -924,6 +924,15 @@ TEST_CASE("ResultReport_LeftoverLattices", "[Diagnostics]") {
     CHECK(text.find("EXTRA_LATTICE_1_MISORIENTATION_DEG") == std::string::npos);
     CHECK(text.find("MULTIPLE_LATTICES= FALSE") != std::string::npos);
 
+    // An unrelated cell is listed but not warned about: it is as often a wrong main lattice or tNCS.
+    LeftoverLattice foreign{.kind = LeftoverLatticeKind::Foreign, .cell = *result.consensus_cell,
+                            .volume_ratio = 1.34, .misorientation_deg = NAN, .z = 40.0,
+                            .spots_pct = 20.0, .intensity_pct = 30.0, .sweep_concentration = 0.3};
+    result.leftover_lattices->lattices = {foreign};
+    text = RenderResultReport("p", "in.h5", x, result);
+    CHECK(text.find("EXTRA_LATTICE_1_KIND= FOREIGN") != std::string::npos);
+    CHECK(text.find("MULTIPLE_LATTICES= FALSE") != std::string::npos);
+
     LeftoverLattice domain{.kind = LeftoverLatticeKind::Domain, .cell = *result.consensus_cell,
                            .volume_ratio = 1.0, .misorientation_deg = 2.7, .z = 250.0,
                            .spots_pct = 20.0, .intensity_pct = 25.0, .sweep_concentration = 0.3};