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>

image_analysis/indexing/IndexerThreadPool.cpp

@@ -222,6 +222,42 @@ IndexerResult IndexerThreadPool::Run(const DiffractionExperiment &experiment, co
                               "Internal error: indexing algorithm must be resolved (not Auto) "
                               "before reaching the indexer pool");
 
+    // The workers built their indexers from the raw requested algorithm, but the algorithm actually
+    // dispatched is the RESOLVED one (rotation, for instance, always resolves to the GPU FFT indexer
+    // when a GPU is present, ignoring the request). If the resolution lands on an algorithm this host
+    // did not build an indexer for, fail here with an explanation instead of the opaque "no indexer
+    // available for the resolved algorithm" from deep inside a worker.
+    const auto requested = experiment.GetIndexingSettings().GetAlgorithm();
+    const bool have_gpu = get_gpu_count() > 0;
+#ifdef JFJOCH_USE_FFTW
+    constexpr bool fftw_built = true;
+#else
+    constexpr bool fftw_built = false;
+#endif
+    const bool servable =
+        (algorithm == IndexingAlgorithmEnum::FFT    && have_gpu &&
+             (requested == IndexingAlgorithmEnum::Auto || requested == IndexingAlgorithmEnum::FFT)) ||
+        (algorithm == IndexingAlgorithmEnum::FFBIDX && have_gpu &&
+             (requested == IndexingAlgorithmEnum::Auto || requested == IndexingAlgorithmEnum::FFBIDX)) ||
+        (algorithm == IndexingAlgorithmEnum::FFTW   && fftw_built &&
+             ((requested == IndexingAlgorithmEnum::Auto && !have_gpu) || requested == IndexingAlgorithmEnum::FFTW));
+    if (!servable) {
+        std::string msg;
+        if (requested == IndexingAlgorithmEnum::FFTW && have_gpu)
+            msg = "FFTW is the CPU indexer and is not available on a node with a GPU. Rotation indexing "
+                  "always uses the GPU FFT indexer here; select FFT or Auto, or run FFTW on a CPU-only node.";
+        else if (algorithm == IndexingAlgorithmEnum::FFT && !have_gpu)
+            msg = "FFT is the GPU indexer but no GPU is available. Select FFTW or Auto for CPU indexing.";
+        else if (algorithm == IndexingAlgorithmEnum::FFBIDX && !have_gpu)
+            msg = "FFBIDX is a GPU indexer but no GPU is available. Select FFTW or Auto for CPU indexing.";
+        else if (algorithm == IndexingAlgorithmEnum::FFTW)
+            msg = "FFTW (CPU) indexing was requested but this build has no FFTW indexer.";
+        else
+            msg = "the requested indexing algorithm resolved to one with no indexer available on this host.";
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Cannot index: " + msg);
+    }
+
     // Check if there is available worker
    const int task = GetFreeWorker();