v1.0.0-rc.160 (#70)

This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.

* rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell.
* rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged.
* rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set.
* rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme.
* rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free.
* rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry.
* Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md.
* Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

tests/IndexingUnitTest.cpp

@@ -246,14 +246,14 @@ TEST_CASE("FFTIndexer","[Indexing]") {
     logger.Info("Time: {} ms", std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count());
 }
 
-TEST_CASE("PostIndexingRefinement_MultiLattice_TwoLysozymes_BraggPrediction","[Indexing]") {
-    Logger logger("PostIndexingRefinement_MultiLattice_TwoLysozymes_BraggPrediction");
+TEST_CASE("PostIndexingRefinement_MultiLattice_TwoCrystals_BraggPrediction","[Indexing]") {
+    Logger logger("PostIndexingRefinement_MultiLattice_TwoCrystals_BraggPrediction");
 
-    UnitCell lysozyme_uc{36.9, 78.95, 78.95, 90.0, 90.0, 90.0};
-    CrystalLattice lysozyme_base(lysozyme_uc);
+    UnitCell tetragonal_uc{36.9, 78.95, 78.95, 90.0, 90.0, 90.0};
+    CrystalLattice tetragonal_base(tetragonal_uc);
 
-    CrystalLattice lysozyme_rot_1 = RotateLattice(lysozyme_base, MakeRotation(10.0f, 18.0f, 27.0f));
-    CrystalLattice lysozyme_rot_2 = RotateLattice(lysozyme_base, MakeRotation(66.0f, -14.0f, 101.0f));
+    CrystalLattice crystal_rot_1 = RotateLattice(tetragonal_base, MakeRotation(10.0f, 18.0f, 27.0f));
+    CrystalLattice crystal_rot_2 = RotateLattice(tetragonal_base, MakeRotation(66.0f, -14.0f, 101.0f));
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.DetectorDistance_mm(75)
@@ -272,8 +272,8 @@ TEST_CASE("PostIndexingRefinement_MultiLattice_TwoLysozymes_BraggPrediction","[I
         .mosaicity_multiplier = 4.0f
     };
 
-    const auto spots_1 = BuildPredictedReciprocalSpots(experiment, lysozyme_rot_1, pred_settings);
-    const auto spots_2 = BuildPredictedReciprocalSpots(experiment, lysozyme_rot_2, pred_settings);
+    const auto spots_1 = BuildPredictedReciprocalSpots(experiment, crystal_rot_1, pred_settings);
+    const auto spots_2 = BuildPredictedReciprocalSpots(experiment, crystal_rot_2, pred_settings);
 
     logger.Info("Predicted spots lattice 1: {}", spots_1.size());
     logger.Info("Predicted spots lattice 2: {}", spots_2.size());
@@ -300,9 +300,9 @@ TEST_CASE("PostIndexingRefinement_MultiLattice_TwoLysozymes_BraggPrediction","[I
         oCell(idx * 3 + 2, 2) = lattice.Vec2().z;
     };
 
-    put_lattice(0, lysozyme_rot_1);
-    put_lattice(1, lysozyme_rot_2);
-    put_lattice(2, lysozyme_rot_1); // duplicate to verify overlap rejection
+    put_lattice(0, crystal_rot_1);
+    put_lattice(1, crystal_rot_2);
+    put_lattice(2, crystal_rot_1); // duplicate to verify overlap rejection
 
     // Keep bootstrap scores tiny to disable candidate drift in iterative re-fitting.
     scores(0) = 1e-6f;
@@ -324,12 +324,12 @@ TEST_CASE("PostIndexingRefinement_MultiLattice_TwoLysozymes_BraggPrediction","[I
 
     REQUIRE(refined.size() >= 2);
 
-    int lysozyme_count = 0;
+    int crystal_count = 0;
     for (const auto &lattice : refined) {
-        if (MatchesCellLengths(lattice.GetUnitCell(), lysozyme_uc))
-            ++lysozyme_count;
+        if (MatchesCellLengths(lattice.GetUnitCell(), tetragonal_uc))
+            ++crystal_count;
     }
-    CHECK(lysozyme_count >= 2);
+    CHECK(crystal_count >= 2);
 
     int64_t count_0 = 0;
     int64_t count_1 = 0;
@@ -346,14 +346,14 @@ TEST_CASE("PostIndexingRefinement_MultiLattice_TwoLysozymes_BraggPrediction","[I
 }
 
 /*
-TEST_CASE("FFTIndexer_MultiLattice_TwoLysozymes_BraggPrediction","[Indexing]") {
-    Logger logger("FFTIndexer_MultiLattice_TwoLysozymes_BraggPrediction");
+TEST_CASE("FFTIndexer_MultiLattice_TwoCrystals_BraggPrediction","[Indexing]") {
+    Logger logger("FFTIndexer_MultiLattice_TwoCrystals_BraggPrediction");
 
-    UnitCell lysozyme_uc{36.9, 78.95, 78.95, 90.0, 90.0, 90.0};
-    CrystalLattice lysozyme_base(lysozyme_uc);
+    UnitCell tetragonal_uc{36.9, 78.95, 78.95, 90.0, 90.0, 90.0};
+    CrystalLattice tetragonal_base(tetragonal_uc);
 
-    CrystalLattice lysozyme_rot_1 = RotateLattice(lysozyme_base, MakeRotation(10.0f, 18.0f, 27.0f));
-    CrystalLattice lysozyme_rot_2 = RotateLattice(lysozyme_base, MakeRotation(66.0f, -14.0f, 101.0f));
+    CrystalLattice crystal_rot_1 = RotateLattice(tetragonal_base, MakeRotation(10.0f, 18.0f, 27.0f));
+    CrystalLattice crystal_rot_2 = RotateLattice(tetragonal_base, MakeRotation(66.0f, -14.0f, 101.0f));
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.DetectorDistance_mm(75)
@@ -372,8 +372,8 @@ TEST_CASE("FFTIndexer_MultiLattice_TwoLysozymes_BraggPrediction","[Indexing]") {
         .mosaicity_multiplier = 4.0f
     };
 
-    auto spots_1 = BuildPredictedReciprocalSpots(experiment, lysozyme_rot_1, pred_settings);
-    auto spots_2 = BuildPredictedReciprocalSpots(experiment, lysozyme_rot_2, pred_settings);
+    auto spots_1 = BuildPredictedReciprocalSpots(experiment, crystal_rot_1, pred_settings);
+    auto spots_2 = BuildPredictedReciprocalSpots(experiment, crystal_rot_2, pred_settings);
 
     logger.Info("Predicted spots lattice 1: {}", spots_1.size());
     logger.Info("Predicted spots lattice 2: {}", spots_2.size());
@@ -389,7 +389,7 @@ TEST_CASE("FFTIndexer_MultiLattice_TwoLysozymes_BraggPrediction","[Indexing]") {
             .FFT_HighResolution_A(2.0f)
             .FFT_NumVectors(1024);
     experiment.ImportIndexingSettings(settings)
-              .SetUnitCell(lysozyme_uc);
+              .SetUnitCell(tetragonal_uc);
 
     REQUIRE(experiment.GetIndexingAlgorithm() == IndexingAlgorithmEnum::FFT);
 
@@ -404,20 +404,20 @@ TEST_CASE("FFTIndexer_MultiLattice_TwoLysozymes_BraggPrediction","[Indexing]") {
 
     const float tolerance = experiment.GetIndexingSettings().GetTolerance();
 
-    int lysozyme_count = 0;
+    int crystal_count = 0;
     for (size_t i = 0; i < result.lattice.size(); ++i) {
         auto uc = result.lattice[i].GetUnitCell();
         int64_t indexed_count = 0;
         BuildIndexedMask(spots, result.lattice[i], tolerance, indexed_count);
         logger.Info("Lattice {} cell ({:.1f} {:.1f} {:.1f}) indexes {} spots",
                     i, uc.a, uc.b, uc.c, indexed_count);
-        if (MatchesCellLengths(uc, lysozyme_uc))
-            ++lysozyme_count;
+        if (MatchesCellLengths(uc, tetragonal_uc))
+            ++crystal_count;
     }
 
-    CHECK(lysozyme_count >= 2);
+    CHECK(crystal_count >= 2);
 
-    // Verify the two best lysozyme lattices are distinct (low overlap)
+    // Verify the two best crystal lattices are distinct (low overlap)
     if (result.lattice.size() >= 2) {
         int64_t count_0 = 0, count_1 = 0;
         auto mask_0 = BuildIndexedMask(spots, result.lattice[0], tolerance, count_0);
@@ -429,14 +429,14 @@ TEST_CASE("FFTIndexer_MultiLattice_TwoLysozymes_BraggPrediction","[Indexing]") {
     }
 }
 
-TEST_CASE("FFBIDXIndexer_MultiLattice_TwoLysozymes_BraggPrediction","[Indexing]") {
-    Logger logger("FFBIDXIndexer_MultiLattice_TwoLysozymes_BraggPrediction");
+TEST_CASE("FFBIDXIndexer_MultiLattice_TwoCrystals_BraggPrediction","[Indexing]") {
+    Logger logger("FFBIDXIndexer_MultiLattice_TwoCrystals_BraggPrediction");
 
-    UnitCell lysozyme_uc{36.9, 78.95, 78.95, 90.0, 90.0, 90.0};
-    CrystalLattice lysozyme_base(lysozyme_uc);
+    UnitCell tetragonal_uc{36.9, 78.95, 78.95, 90.0, 90.0, 90.0};
+    CrystalLattice tetragonal_base(tetragonal_uc);
 
-    CrystalLattice lysozyme_rot_1 = RotateLattice(lysozyme_base, MakeRotation(10.0f, 18.0f, 27.0f));
-    CrystalLattice lysozyme_rot_2 = RotateLattice(lysozyme_base, MakeRotation(66.0f, -14.0f, 101.0f));
+    CrystalLattice crystal_rot_1 = RotateLattice(tetragonal_base, MakeRotation(10.0f, 18.0f, 27.0f));
+    CrystalLattice crystal_rot_2 = RotateLattice(tetragonal_base, MakeRotation(66.0f, -14.0f, 101.0f));
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.DetectorDistance_mm(75)
@@ -455,8 +455,8 @@ TEST_CASE("FFBIDXIndexer_MultiLattice_TwoLysozymes_BraggPrediction","[Indexing]"
         .mosaicity_multiplier = 4.0f
     };
 
-    auto spots_1 = BuildPredictedReciprocalSpots(experiment, lysozyme_rot_1, pred_settings);
-    auto spots_2 = BuildPredictedReciprocalSpots(experiment, lysozyme_rot_2, pred_settings);
+    auto spots_1 = BuildPredictedReciprocalSpots(experiment, crystal_rot_1, pred_settings);
+    auto spots_2 = BuildPredictedReciprocalSpots(experiment, crystal_rot_2, pred_settings);
 
     logger.Info("Predicted spots lattice 1: {}", spots_1.size());
     logger.Info("Predicted spots lattice 2: {}", spots_2.size());
@@ -466,7 +466,7 @@ TEST_CASE("FFBIDXIndexer_MultiLattice_TwoLysozymes_BraggPrediction","[Indexing]"
     spots.insert(spots.end(), spots_1.begin(), spots_1.end());
     spots.insert(spots.end(), spots_2.begin(), spots_2.end());
 
-    experiment.SetUnitCell(lysozyme_uc);
+    experiment.SetUnitCell(tetragonal_uc);
     experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFBIDX);
 
     REQUIRE(experiment.GetIndexingAlgorithm() == IndexingAlgorithmEnum::FFBIDX);
@@ -482,20 +482,20 @@ TEST_CASE("FFBIDXIndexer_MultiLattice_TwoLysozymes_BraggPrediction","[Indexing]"
 
     const float tolerance = experiment.GetIndexingSettings().GetTolerance();
 
-    int lysozyme_count = 0;
+    int crystal_count = 0;
     for (size_t i = 0; i < result.lattice.size(); ++i) {
         auto uc = result.lattice[i].GetUnitCell();
         int64_t indexed_count = 0;
         BuildIndexedMask(spots, result.lattice[i], tolerance, indexed_count);
         logger.Info("Lattice {} cell ({:.1f} {:.1f} {:.1f}) indexes {} spots",
                     i, uc.a, uc.b, uc.c, indexed_count);
-        if (MatchesCellLengths(uc, lysozyme_uc))
-            ++lysozyme_count;
+        if (MatchesCellLengths(uc, tetragonal_uc))
+            ++crystal_count;
     }
 
-    CHECK(lysozyme_count >= 2);
+    CHECK(crystal_count >= 2);
 
-    // Verify the two best lysozyme lattices are distinct (low overlap)
+    // Verify the two best crystal lattices are distinct (low overlap)
     if (result.lattice.size() >= 2) {
         int64_t count_0 = 0, count_1 = 0;
         auto mask_0 = BuildIndexedMask(spots, result.lattice[0], tolerance, count_0);