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Indexing: a coplanar cell leaves the frame unindexed instead of throwing

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The online broker cancelled a collection with "Crystal lattice is coplanar and has no reciprocal
cell". The candidate filter in PostIndexingRefinement (used by FFT, FFTW and ffbidx) tests lengths,
angles and spot count only; three rows 120 deg apart in one plane pass all of them, and spots along
the plane normal index as (0,0,0). Such a candidate - from ffbidx, or one the least-squares
refinement walked flat - went on to LatticeSearch and XtalOptimizer, which refuses it and leaves it
in place, and then reached Astar() in AnalyzeIndexing/prediction, which throws; the receiver turns
that into a cancelled acquisition.

- Refine() rejects a candidate below MIN_BASIS_VOLUME_FRACTION, like any other bad candidate.
- XtalOptimizerInternal builds the refined lattice first and counts a coplanar result as a failed
  refinement, writing nothing back (the residual's volume clamp lets a solve end there and report
  success).

Test: PostIndexingRefinement_CoplanarCandidateIsRejected threw the exact message before the fix.
rugnux p.mtz unchanged on the three in-house reference sets at --prepass-fraction 1.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
This commit is contained in:
leonarski_f
2026-10-07 13:55:44 +02:00
co-authored by Claude Opus 5.5
parent 280ff0a4a0
commit e6bbfea4c4
3 changed files with 72 additions and 18 deletions
Download Patch File Download Diff File Expand all files Collapse all files
image_analysis/geom_refinement/XtalOptimizer.cpp
+26 -18
View File
@@ -457,6 +457,31 @@ bool XtalOptimizerInternal(XtalOptimizerData &data,
if (!summary.IsSolutionUsable())
return false;
// A solve can walk the basis flat and still report success - the volume clamp in XtalResidual
// keeps every step finite on the way. A coplanar cell has no reciprocal basis, so that is a
// failed refinement: refuse it like any other, before anything is written back.
CrystalLattice latt;
if (data.crystal_system == gemmi::CrystalSystem::Orthorhombic)
latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, PI / 2.0, PI / 2.0);
else if (data.crystal_system == gemmi::CrystalSystem::Tetragonal) {
latt_vec1[1] = latt_vec1[0];
latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, PI / 2.0, PI / 2.0);
} else if (data.crystal_system == gemmi::CrystalSystem::Cubic) {
latt_vec1[1] = latt_vec1[0];
latt_vec1[2] = latt_vec1[0];
latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, PI / 2.0, PI / 2.0);
} else if (data.crystal_system == gemmi::CrystalSystem::Hexagonal) {
latt_vec1[1] = latt_vec1[0];
latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1,PI / 2.0, PI / 2.0, 2.0 * PI / 3.0);
} else if (data.crystal_system == gemmi::CrystalSystem::Monoclinic) {
latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, latt_vec2[0], PI / 2.0);
} else {
// Triclinic via the same generic builder
latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, latt_vec2[0], latt_vec2[1], latt_vec2[2]);
}
if (latt.VolumeFraction() < MIN_BASIS_VOLUME_FRACTION)
return false;
if (data.refine_beam_center) {
data.beam_corr_x = data.geom.GetBeamX_pxl() - beam[0];
data.beam_corr_y = data.geom.GetBeamY_pxl() - beam[1];
@@ -470,24 +495,7 @@ bool XtalOptimizerInternal(XtalOptimizerData &data,
if (data.axis && data.refine_rotation_axis)
data.axis.value().Axis(Coord(rot_vec[0], rot_vec[1], rot_vec[2]));
if (data.crystal_system == gemmi::CrystalSystem::Orthorhombic)
data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, PI / 2.0, PI / 2.0);
else if (data.crystal_system == gemmi::CrystalSystem::Tetragonal) {
latt_vec1[1] = latt_vec1[0];
data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, PI / 2.0, PI / 2.0);
} else if (data.crystal_system == gemmi::CrystalSystem::Cubic) {
latt_vec1[1] = latt_vec1[0];
latt_vec1[2] = latt_vec1[0];
data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, PI / 2.0, PI / 2.0);
} else if (data.crystal_system == gemmi::CrystalSystem::Hexagonal) {
latt_vec1[1] = latt_vec1[0];
data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1,PI / 2.0, PI / 2.0, 2.0 * PI / 3.0);
} else if (data.crystal_system == gemmi::CrystalSystem::Monoclinic) {
data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, PI / 2.0, latt_vec2[0], PI / 2.0);
} else {
// Triclinic via the same generic builder
data.latt = AngleAxisAndCellToLattice(latt_vec0, latt_vec1, latt_vec2[0], latt_vec2[1], latt_vec2[2]);
}
data.latt = latt;
return true;
} catch (...) {
// Convergence problems, likely not updated
image_analysis/indexing/PostIndexingRefinement.cpp
+6
View File
@@ -270,6 +270,12 @@ std::vector<CrystalLattice> Refine(const std::vector<Coord> &in_spots,
cos_gamma > cos_min_angle || cos_gamma < cos_max_angle)
continue;
// Three coplanar rows pass both tests above - 120 deg apart in one plane is inside any angle
// window - and the refinement can walk a candidate there. Such a cell has no reciprocal basis,
// so it is not a lattice: the same volume test as CrystalLattice::VolumeFraction().
if (std::abs(cell_rows.determinant()) < MIN_BASIS_VOLUME_FRACTION * row_norms.prod())
continue;
int64_t indexed_spot_count = 0;
auto indexed_mask = ComputeIndexedMask(spots.topRows(nspots), cell_cols, p.indexing_tolerance, indexed_spot_count);
tests/IndexingUnitTest.cpp
+40
View File
@@ -785,3 +785,43 @@ TEST_CASE("FitSupercellProbe", "[SupercellProbe]") {
// Too few reflections to fit a line: nothing.
CHECK(FitSupercellProbe(SupercellProbeClass{}).b == 0.0);
}
TEST_CASE("PostIndexingRefinement_CoplanarCandidateIsRejected", "[Indexing]") {
// A candidate whose three rows lie in one plane passes every length and angle test - three rows
// 120 deg apart in a plane meet the 30-150 deg window - and every spot along the plane normal
// indexes as (0,0,0), so the spot count passes too. Such a cell has no reciprocal basis; handed
// on, it made the online analysis throw "Crystal lattice is coplanar" for the frame instead of
// leaving the frame unindexed.
const Coord a(50, 0, 0);
const Coord b(-25, 25.0f * std::sqrt(3.0f), 0);
const Coord c(-25, -25.0f * std::sqrt(3.0f), 0);
REQUIRE(CrystalLattice(a, b, c).VolumeFraction() < MIN_BASIS_VOLUME_FRACTION);
std::vector<Coord> spots;
for (int i = 1; i <= 40; i++)
spots.emplace_back(0.0f, 0.0f, 0.01f * static_cast<float>(i));
Eigen::MatrixX3<float> cells(3, 3);
cells << a.x, a.y, a.z,
b.x, b.y, b.z,
c.x, c.y, c.z;
// A score below the refinement's distance floor, so the candidate reaches the filters as given.
Eigen::VectorX<float> scores(1);
scores << -10.99f;
RefineParameters parameters{
.viable_cell_min_spots = 9,
.dist_tolerance_vs_reference = 0.05,
.reference_unit_cell = std::nullopt,
.min_length_A = 5,
.max_length_A = 500,
.min_angle_deg = 30,
.max_angle_deg = 150,
.indexing_tolerance = 0.1
};
const auto lattices = Refine(spots, spots.size(), cells, scores, parameters);
CHECK(lattices.empty());
for (const auto &l: lattices)
CHECK_NOTHROW(l.GetUBMatrix());
}