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/HDF5WritingTest.cpp

@@ -514,10 +514,10 @@ TEST_CASE("HDF5Writer_Socket", "[HDF5][Full]") {
         x.FrameTime(std::chrono::microseconds(1000), std::chrono::microseconds(100));
 
         DatasetSettings d;
-        d.FilePrefix("run0345_lysozyme_acq").ImagesPerTrigger(5).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION)
+        d.FilePrefix("run0345_acq").ImagesPerTrigger(5).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION)
                 .HeaderAppendix(R"({"z":567})"_json).DetectorDistance_mm(155).BeamX_pxl(1606.62).BeamY_pxl(1669.59)
                 .PhotonEnergy_keV(12.07).SetUnitCell(UnitCell{.a = 97, .b = 97, .c = 38, .alpha= 90, .beta = 90, .gamma = 90})
-                .SpaceGroupNumber(96).RunNumber(345).ExperimentGroup("p12345").SampleName("lysozyme").RunName("run1");
+                .SpaceGroupNumber(96).RunNumber(345).ExperimentGroup("p12345").SampleName("test_sample").RunName("run1");
 
         x.ImportDatasetSettings(d).OverwriteExistingFiles(true);
         std::vector<SpotToSave> spots;
@@ -550,7 +550,7 @@ TEST_CASE("HDF5Writer_Socket", "[HDF5][Full]") {
         REQUIRE(s.Receive(msg, true));
 
         j = nlohmann::json::parse(std::string((char *) msg.data(), msg.size()));
-        REQUIRE(j["filename"] == "run0345_lysozyme_acq_data_000001.h5");
+        REQUIRE(j["filename"] == "run0345_acq_data_000001.h5");
         REQUIRE(j["file_number"] == 1);
         REQUIRE(j["nimages"] == 2);
         REQUIRE(j["incident_energy_eV"] == Catch::Approx(x.GetIncidentEnergy_keV() * 1000.0));
@@ -564,7 +564,7 @@ TEST_CASE("HDF5Writer_Socket", "[HDF5][Full]") {
 
         REQUIRE(s.Receive(msg, true));
         j = nlohmann::json::parse(std::string((char *) msg.data(), msg.size()));
-        REQUIRE(j["filename"] == "run0345_lysozyme_acq_data_000002.h5");
+        REQUIRE(j["filename"] == "run0345_acq_data_000002.h5");
         REQUIRE(j["file_number"] == 2);
         REQUIRE(j["nimages"] == 2);
         REQUIRE(j.contains("user_data"));
@@ -572,7 +572,7 @@ TEST_CASE("HDF5Writer_Socket", "[HDF5][Full]") {
 
         REQUIRE(s.Receive(msg, true));
         j = nlohmann::json::parse(std::string((char *) msg.data(), msg.size()));
-        REQUIRE(j["filename"] == "run0345_lysozyme_acq_data_000003.h5");
+        REQUIRE(j["filename"] == "run0345_acq_data_000003.h5");
         REQUIRE(j["file_number"] == 3);
         REQUIRE(j["nimages"] == 1);
         REQUIRE(j.contains("user_data"));
@@ -1255,101 +1255,6 @@ TEST_CASE("HDF5Writer_Link_zero_images", "[HDF5][Full]") {
     REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
 
-TEST_CASE("FileWriter_CBF_16bit", "[HDF5][Full]") {
-    {
-        DetectorSetup det = DetJF4M("DET1");
-        det.SerialNumber("1");
-        DiffractionExperiment x(det);
-        std::vector<SpotToSave> spots;
-
-        x.FilePrefix("lyso_cbf_16").ImagesPerTrigger(5).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION);
-        x.PixelSigned(true).BitDepthImage(16);
-        x.SetFileWriterFormat(FileWriterFormat::CBF);
-        StartMessage start_message;
-        x.FillMessage(start_message);
-
-        FileWriter file_set(start_message);
-        std::vector<int16_t> image(x.GetPixelsNum(), 45);
-
-        for (int i = 0; i < x.GetImageNum(); i++) {
-            DataMessage message{};
-            message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
-            message.spots = spots;
-            message.number = i;
-
-            REQUIRE_NOTHROW(file_set.Write(message));
-        }
-
-        auto v = file_set.Finalize();
-
-        REQUIRE(!file_set.GetZMQAddr());
-    }
-}
-
-TEST_CASE("FileWriter_CBF", "[HDF5][Full]") {
-    {
-        DetectorSetup det = DetJF4M("DET1");
-        det.SerialNumber("1");
-        DiffractionExperiment x(det);
-        std::vector<SpotToSave> spots;
-
-        x.FilePrefix("lyso_cbf").ImagesPerTrigger(5).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION);
-        x.PixelSigned(false).BitDepthImage(32);
-        x.SetFileWriterFormat(FileWriterFormat::CBF);
-        StartMessage start_message;
-        x.FillMessage(start_message);
-
-        FileWriter file_set(start_message);
-        std::vector<uint32_t> image(x.GetPixelsNum());
-
-        for (int i = 0; i < image.size(); i++)
-            image[i] = i;
-
-        for (int i = 0; i < x.GetImageNum(); i++) {
-            DataMessage message{};
-            message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
-            message.spots = spots;
-            message.number = i;
-
-            REQUIRE_NOTHROW(file_set.Write(message));
-        }
-
-        auto v = file_set.Finalize();
-
-        REQUIRE(!file_set.GetZMQAddr());
-    }
-}
-
-TEST_CASE("FileWriter_TIFF", "[HDF5][Full]") {
-    {
-        DetectorSetup det = DetJF4M("DET1");
-        det.SerialNumber("1");
-        DiffractionExperiment x(det);
-        std::vector<SpotToSave> spots;
-
-        x.FilePrefix("lyso_tiff").ImagesPerTrigger(5).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION);
-        x.SetFileWriterFormat(FileWriterFormat::TIFF);
-        StartMessage start_message;
-        x.FillMessage(start_message);
-
-        FileWriter file_set(start_message);
-        std::vector<int16_t> image(x.GetPixelsNum(), 45);
-
-        for (int i = 0; i < x.GetImageNum(); i++) {
-            DataMessage message{};
-            message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
-            message.spots = spots;
-            message.number = i;
-
-            REQUIRE_NOTHROW(file_set.Write(message));
-        }
-
-        auto v = file_set.Finalize();
-
-        REQUIRE(!file_set.GetZMQAddr());
-    }
-}
-
 TEST_CASE("HDF5Objects_VDS_reverse_contiguous", "[HDF5][Unit]") {
     {
         RegisterHDF5Filter();