Stills with a cell but no space group: keep the cell's angles and setting

With -C and no -S, two things broke a cell whose angles are not all 90 deg:

- DiffractionExperiment::GetCrystalSystem() returned Monoclinic when no
  space group was set, and the stills geometry bundle adjustment (and the
  tilt trial) parametrise the cell by that system, so a hexagonal cell was
  refined with alpha = gamma = 90 deg. The refined cell then fed FFBIDX for
  the whole run: on a trigonal crystal 5.9% of the frames indexed instead of
  16.4%. Without a space group the system is now Triclinic.

- IndexAndRefine replaced the lattice FFBIDX returned on the given cell's
  axes with LatticeSearch's conventional setting, chosen frame by frame, so
  frames of one crystal form landed in different settings (89% of an
  R-centred hexagonal run reported as a second crystal form). The FFBIDX
  lattice is now kept, refined with every angle free.

Runs with -S take the other branch and are unchanged.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UqXYdL4qBGYRiSXSGXfCLu

common/DiffractionExperiment.cpp

@@ -1843,9 +1843,11 @@ DiffractionExperiment &DiffractionExperiment::GeomRefinementAlgorithm(GeomRefine
 }
 
 gemmi::CrystalSystem DiffractionExperiment::GetCrystalSystem() const {
+    // Without a space group nothing is known of the cell's symmetry: triclinic leaves every angle of
+    // the given cell free, where any other system would hold some of them at 90 degrees.
     auto sg = GetGemmiSpaceGroup();
     if (!sg)
-        return gemmi::CrystalSystem::Monoclinic;
+        return gemmi::CrystalSystem::Triclinic;
 
     return sg->crystal_system();
 }

image_analysis/IndexAndRefine.cpp

@@ -380,6 +380,19 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(Data
                 else if (!de_novo)
                     outcome.lattice_candidate = latt;
                 // else: de-novo + symmetry mismatch -> leave unset, frame is not indexed
+            } else if (!de_novo && experiment.GetUnitCell()
+                       && latt.GetUnitCell().is_close(*experiment.GetUnitCell(),
+                                                      experiment.GetIndexingSettings().GetUnitCellDistTolerance(),
+                                                      experiment.GetIndexingSettings().GetUnitCellAngleTolerance_deg())) {
+                // A cell with no space group: FFBIDX returned the lattice on the given cell's axes, and
+                // it stays on them, so that every frame is in one setting. Nothing is known of the
+                // symmetry, so it is refined with every angle free.
+                outcome.symmetry = LatticeMessage{
+                    .centering = 'P',
+                    .niggli_class = 0,
+                    .crystal_system = gemmi::CrystalSystem::Triclinic
+                };
+                outcome.lattice_candidate = latt;
             } else {
                 auto sym_result = LatticeSearch(latt);
                 outcome.symmetry = LatticeMessage{

tests/DiffractionExperimentTest.cpp

@@ -354,7 +354,7 @@ TEST_CASE("DiffractionExperiment_ZMQPreview", "[DiffractionExperiment]") {
 TEST_CASE("DiffractionExperiment_SpaceGroup", "[DiffractionExperiment]") {
     DiffractionExperiment x;
     REQUIRE(!x.GetGemmiSpaceGroup());
-    REQUIRE(x.GetCrystalSystem() == gemmi::CrystalSystem::Monoclinic);
+    REQUIRE(x.GetCrystalSystem() == gemmi::CrystalSystem::Triclinic);
     REQUIRE_THROWS(x.SpaceGroupNumber(-1));
     REQUIRE_THROWS(x.SpaceGroupNumber(500));
     REQUIRE_NOTHROW(x.SpaceGroupNumber(96));