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/CBORTest.cpp

@@ -40,8 +40,8 @@ TEST_CASE("CBORSerialize_Start", "[CBOR]") {
         .storage_cell_delay_ns = 15345,
         .pixel_mask_enabled = true,
         .arm_date = "abc",
-        .sample_name = "lyso",
-        .file_prefix = "lyso1/dir/file",
+        .sample_name = "test_sample",
+        .file_prefix = "test_sample/dir/file",
         .images_per_file = 12345,
         .channels = {"default", "sc2"},
         .detector_description = "EIGER 16M",

tests/DiffractionExperimentTest.cpp

@@ -365,8 +365,8 @@ TEST_CASE("DiffractionExperiment_SampleName", "[DiffractionExperiment]") {
     REQUIRE_NOTHROW(x.SampleName(""));
     REQUIRE(x.GetSampleName().empty());
 
-    REQUIRE_NOTHROW(x.SampleName("lyso1"));
-    REQUIRE(x.GetSampleName() == "lyso1");
+    REQUIRE_NOTHROW(x.SampleName("test_sample"));
+    REQUIRE(x.GetSampleName() == "test_sample");
 }
 
 TEST_CASE("DiffractionExperiment_SaveCalibration", "[DiffractionExperiment]") {

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();

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);

tests/JFJochReaderTest.cpp

@@ -1473,7 +1473,7 @@ TEST_CASE("JFJochReader_InstrumentMetadata_Sample_RingCurrent", "[HDF5][Full]")
 
     InstrumentMetadata metadata;
     metadata.InstrumentName("PXI").SourceName("SLS");
-    x.ImportInstrumentMetadata(metadata).SampleName("Lysozyme").RingCurrent_mA(399.5); // 0.3995 A
+    x.ImportInstrumentMetadata(metadata).SampleName("test_sample").RingCurrent_mA(399.5); // 0.3995 A
     x.TotalFlux(1e7).AttenuatorTransmission(0.56);
     x.DetectIceRings(false);
 
@@ -1511,7 +1511,7 @@ TEST_CASE("JFJochReader_InstrumentMetadata_Sample_RingCurrent", "[HDF5][Full]")
         CHECK(dataset->experiment.GetTotalFlux() == Catch::Approx(1e7));
 
         // Sample name
-        CHECK(dataset->experiment.GetSampleName() == "Lysozyme");
+        CHECK(dataset->experiment.GetSampleName() == "test_sample");
 
         // Ring current read back in mA; allow small fp tolerance
         CHECK(dataset->experiment.GetRingCurrent_mA().has_value());

tests/JFJochReceiverLiteTest.cpp

@@ -21,7 +21,7 @@ TEST_CASE("JFJochReceiverLite", "[JFJochReceiver]") {
     DiffractionExperiment experiment(DetDECTRIS(2068, 2164, "Test", {}));
 
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_lite").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
+            .FilePrefix("crystal_test_lite").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
                     FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
@@ -99,7 +99,7 @@ TEST_CASE("JFJochReceiverLite", "[JFJochReceiver]") {
 }
 
 TEST_CASE("JFJochReceiverLite_Cancel", "[JFJochReceiver]") {
-    Logger logger("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index");
+    Logger logger("JFJochReceiverLite_Cancel");
 
     RegisterHDF5Filter();
 
@@ -108,7 +108,7 @@ TEST_CASE("JFJochReceiverLite_Cancel", "[JFJochReceiver]") {
     DiffractionExperiment experiment(DetDECTRIS(2068, 2164, "Test", {}));
 
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_lite").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
+            .FilePrefix("crystal_test_lite").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
                     FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});

tests/JFJochReceiverProcessingTest.cpp

@@ -17,7 +17,7 @@
 #include "../image_pusher/TCPStreamPusher.h"
 #include "../image_puller/TCPImagePuller.h"
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -26,7 +26,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
+            .FilePrefix("crystal_test").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
     experiment.SampleTemperature_K(123.0).RingCurrent_mA(115);
@@ -92,7 +92,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
     };
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
     REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     CHECK(receiver_out.efficiency == 1.0);
@@ -107,7 +107,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_refinement", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -116,7 +116,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement", "[JFJo
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_refinement").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
+            .FilePrefix("crystal_test_refinement").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
                     FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90})
@@ -184,7 +184,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement", "[JFJo
     };
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
     REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     CHECK(receiver_out.efficiency == 1.0);
@@ -199,7 +199,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement", "[JFJo
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement_tetragonal", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_refinement_tetragonal", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -208,7 +208,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement_tetragon
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_refinement_tetragonal").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
+            .FilePrefix("crystal_test_refinement_tetragonal").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
                     FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 78.95, .b = 78.95, .c = 36.9, .alpha = 90, .beta = 90, .gamma = 90})
@@ -277,7 +277,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement_tetragon
     };
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
     REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     CHECK(receiver_out.efficiency == 1.0);
@@ -292,7 +292,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_refinement_tetragon
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_index_and_integrate", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -301,7 +301,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate", "[JFJoc
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
+            .FilePrefix("crystal_test").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
     PixelMask pixel_mask(experiment);
@@ -366,7 +366,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate", "[JFJoc
     };
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
     REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     CHECK(receiver_out.efficiency == 1.0);
@@ -388,7 +388,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate", "[JFJoc
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate_no_spots", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_index_and_integrate_no_spots", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -397,7 +397,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate_no_spots"
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
+            .FilePrefix("crystal_test").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
     PixelMask pixel_mask(experiment);
@@ -465,7 +465,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_index_and_integrate_no_spots"
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_azint_2d", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_azint_2d", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -474,7 +474,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_azint_2d", "[JFJochReceiver]") {
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_azim_2d").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
+            .FilePrefix("crystal_test_azim_2d").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
     PixelMask pixel_mask(experiment);
@@ -542,7 +542,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_azint_2d", "[JFJochReceiver]") {
     REQUIRE(azim_plot.GetPlots()[0].z.size() == 120 * 16);
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_FFT", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -551,7 +551,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT", "[JFJochRecei
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_fft").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
+            .FilePrefix("crystal_test_fft").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
             .OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .IndexingAlgorithm(IndexingAlgorithmEnum::FFT);
@@ -616,7 +616,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT", "[JFJochRecei
     };
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
     REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     CHECK(receiver_out.efficiency == 1.0);
@@ -631,7 +631,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT", "[JFJochRecei
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFTW", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_FFTW", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -640,7 +640,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFTW", "[JFJochRece
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_fftw").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
+            .FilePrefix("crystal_test_fftw").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
             .OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .IndexingAlgorithm(IndexingAlgorithmEnum::FFTW);
@@ -705,7 +705,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFTW", "[JFJochRece
     };
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
     REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     CHECK(receiver_out.efficiency == 1.0);
@@ -720,7 +720,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFTW", "[JFJochRece
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_reference", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_FFT_reference", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -729,7 +729,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_reference", "[J
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_fft_ref").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
+            .FilePrefix("crystal_test_fft_ref").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
             .OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .IndexingAlgorithm(IndexingAlgorithmEnum::FFT)
@@ -795,7 +795,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_reference", "[J
     };
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
     REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     CHECK(receiver_out.efficiency == 1.0);
@@ -810,7 +810,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_reference", "[J
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_wrong_reference", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_FFT_wrong_reference", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -819,7 +819,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_wrong_reference
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_fft_wrongref").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
+            .FilePrefix("crystal_test_fft_wrongref").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS)
             .OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .IndexingAlgorithm(IndexingAlgorithmEnum::FFT)
@@ -885,7 +885,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_wrong_reference
     };
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
     REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     CHECK(receiver_out.efficiency == 1.0);
@@ -900,7 +900,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_FFT_wrong_reference
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_grid", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_grid", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -916,7 +916,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_grid", "[JFJochRece
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.UseInternalPacketGenerator(true).ImagesPerFile(2).ImportDatasetSettings(dataset_settings)
-            .FilePrefix("lyso_test_grid").JungfrauConvPhotonCnt(false)
+            .FilePrefix("crystal_test_grid").JungfrauConvPhotonCnt(false)
             .SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true);
     PixelMask pixel_mask(experiment);
 
@@ -1010,7 +1010,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_grid", "[JFJochRece
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_32", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -1019,7 +1019,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiv
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_32").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxLegacy).OverwriteExistingFiles(true)
+            .FilePrefix("crystal_test_32").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxLegacy).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4).BitDepthImage(32).PixelSigned(true)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
     PixelMask pixel_mask(experiment);
@@ -1082,7 +1082,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiv
     };
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
     REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_min_pix_1.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_min_pix_1.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     CHECK(receiver_out.efficiency == 1.0);
@@ -1097,7 +1097,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_32", "[JFJochReceiv
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_ZMQ_crystal_spot_and_index_min_pix_2", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -1106,7 +1106,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).OverwriteExistingFiles(true)
-            .FilePrefix("lyso_test_min_pix_2").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
+            .FilePrefix("crystal_test_min_pix_2").JungfrauConvPhotonCnt(false).SetFileWriterFormat(
                     FileWriterFormat::NXmxVDS)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90})
@@ -1164,7 +1164,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
     };
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
     REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_min_pix_2.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_min_pix_2.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     REQUIRE_NOTHROW(jpeg_indexed = service.GetJPEGFromBuffer(jpeg_settings, ImageBuffer::MaxIndexedImage));
@@ -1181,7 +1181,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
 TEST_CASE("GenerateResolutionMap") {
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
-            .FilePrefix("lyso_test").JungfrauConvPhotonCnt(false)
+            .FilePrefix("crystal_test").JungfrauConvPhotonCnt(false)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
 
@@ -1211,7 +1211,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
-            .FilePrefix("lyso_test_roi").JungfrauConvPhotonCnt(false)
+            .FilePrefix("crystal_test_roi").JungfrauConvPhotonCnt(false)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90})
             .SetFileWriterFormat(FileWriterFormat::NXmxVDS).PixelSigned(true).OverwriteExistingFiles(true);
@@ -1297,7 +1297,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
     REQUIRE_NOTHROW(jpeg = service.GetJPEGFromBuffer(jpeg_settings));
 
    REQUIRE(!jpeg.empty());
-    std::ofstream f("lyso_processing_test_roi.jpeg", std::ios::binary);
+    std::ofstream f("crystal_processing_test_roi.jpeg", std::ios::binary);
     f.write(jpeg.data(), jpeg.size());
 
     auto plot = service.GetDataProcessingPlot(PlotRequest{.type = PlotType::ROISum, .binning = 1});
@@ -1543,41 +1543,6 @@ TEST_CASE("JFJochIntegrationTest_HDF5FilePusher_republish", "[JFJochReceiver]")
     REQUIRE(!pull_socket.Receive(msg, true));
 }
 
-TEST_CASE("JFJochIntegrationTest_HDF5FilePusher_cbf", "[JFJochReceiver]") {
-    Logger logger(Catch::getResultCapture().getCurrentTestName());
-
-    RegisterHDF5Filter();
-
-    const uint16_t nthreads = 4;
-
-    DiffractionExperiment experiment(DetJF4M());
-    experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
-            .FilePrefix("cbf_test").JungfrauConvPhotonCnt(true)
-            .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
-            .SetFileWriterFormat(FileWriterFormat::CBF);
-
-    JFCalibration calibration(experiment);
-    PixelMask pixel_mask(experiment);
-
-    // Setup acquisition device
-    AcquisitionDeviceGroup aq_devices;
-    aq_devices.Add(std::make_unique<HLSSimulatedDevice>(0, 64));
-
-    HDF5FilePusher pusher;
-
-    JFJochReceiverService service(aq_devices, logger, pusher);
-    service.NumThreads(nthreads);
-    service.Indexing(experiment.GetIndexingSettings());
-
-    service.Start(experiment, pixel_mask, &calibration);
-    auto receiver_out = service.Stop();
-
-    CHECK(receiver_out.efficiency == 1.0);
-    CHECK(receiver_out.status.images_collected == 5);
-    CHECK(receiver_out.status.images_sent == 5);
-    CHECK(!receiver_out.status.cancelled);
-}
-
 TEST_CASE("JFJochIntegrationTest_HDF5FilePusher_Raw", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
@@ -1612,7 +1577,7 @@ TEST_CASE("JFJochIntegrationTest_HDF5FilePusher_Raw", "[JFJochReceiver]") {
     CHECK(!receiver_out.status.cancelled);
 }
 
-TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_no_processing", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_TCP_crystal_no_processing", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -1621,7 +1586,7 @@ TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_no_processing", "[JFJochReceiver]"
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_tcp_no_processing").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
+            .FilePrefix("crystal_test_tcp_no_processing").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
     experiment.SampleTemperature_K(123.0).RingCurrent_mA(115);
@@ -1689,7 +1654,7 @@ TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_no_processing", "[JFJochReceiver]"
     CHECK(ack == experiment.GetImageNum());
 }
 
-TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_spot_and_index", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_TCP_crystal_spot_and_index", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -1698,7 +1663,7 @@ TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_spot_and_index", "[JFJochReceiver]
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_tcp").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
+            .FilePrefix("crystal_test_tcp").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxVDS).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
     experiment.SampleTemperature_K(123.0).RingCurrent_mA(115);
@@ -1831,7 +1796,7 @@ TEST_CASE("JFJochIntegrationTest_TCP_calibration", "[JFJochReceiver]") {
     REQUIRE_NOTHROW(writer_future.get());
 }
 
-TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_spot_and_index_single_file", "[JFJochReceiver]") {
+TEST_CASE("JFJochIntegrationTest_TCP_crystal_spot_and_index_single_file", "[JFJochReceiver]") {
     Logger logger(Catch::getResultCapture().getCurrentTestName());
 
     RegisterHDF5Filter();
@@ -1840,7 +1805,7 @@ TEST_CASE("JFJochIntegrationTest_TCP_lysozyme_spot_and_index_single_file", "[JFJ
 
     DiffractionExperiment experiment(DetJF4M());
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true).ImagesPerFile(2)
-            .FilePrefix("lyso_test_tcp_single_file").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxIntegrated).OverwriteExistingFiles(true)
+            .FilePrefix("crystal_test_tcp_single_file").JungfrauConvPhotonCnt(false).SetFileWriterFormat(FileWriterFormat::NXmxIntegrated).OverwriteExistingFiles(true)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
     experiment.SampleTemperature_K(123.0).RingCurrent_mA(115);

tests/RugnuxLargeTest.cpp

@@ -25,7 +25,7 @@ namespace {
     public:
         using Catch::EventListenerBase::EventListenerBase;
         void testRunStarting(Catch::TestRunInfo const &) override {
-            const bool rot = jfjoch_test::LargeDataFile("lyso_rotation_master.h5").has_value();
+            const bool rot = jfjoch_test::LargeDataFile("rotation_master.h5").has_value();
             std::cout << "[jfjoch_test] large dataset in " << jfjoch_test::LargeDataDir()
                       << ": rotation=" << (rot ? "yes" : "no")
                       << " ([large] tests skip when absent)" << std::endl;
@@ -40,10 +40,10 @@ namespace {
 
 CATCH_REGISTER_LISTENER(LargeDataListener)
 
-TEST_CASE("Rugnux_LysoRotation", "[large]") {
-    const auto master = jfjoch_test::LargeDataFile("lyso_rotation_master.h5");
+TEST_CASE("Rugnux_Rotation", "[large]") {
+    const auto master = jfjoch_test::LargeDataFile("rotation_master.h5");
     if (!master)
-        SKIP("lyso_rotation_master.h5 not available (git-lfs data not pulled)");
+        SKIP("rotation_master.h5 not available (git-lfs data not pulled)");
 
     RegisterHDF5Filter();
     JFJochHDF5Reader reader;

tests/RugnuxTest.cpp

@@ -151,7 +151,7 @@ TEST_CASE("RugnuxCommandLine_Full", "[process]") {
     config.rotation_indexing_image_count = 30;
     config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
 
-    const std::string cmd = RugnuxCommandLine(config, x, "/data/lyso_master.h5");
+    const std::string cmd = RugnuxCommandLine(config, x, "/data/test_master.h5");
     CHECK(cmd.rfind("rugnux", 0) == 0);
     CHECK(cmd.find("-N 8") != std::string::npos);
     CHECK(cmd.find("-e 500") != std::string::npos);
@@ -162,7 +162,7 @@ TEST_CASE("RugnuxCommandLine_Full", "[process]") {
     // would not re-parse (getopt would leave 30 as a positional and drop the count).
     CHECK(cmd.find("-R30") != std::string::npos);
     CHECK(cmd.find("-R 30") == std::string::npos);
-    CHECK(cmd.find("/data/lyso_master.h5") != std::string::npos);
+    CHECK(cmd.find("/data/test_master.h5") != std::string::npos);
 }
 
 TEST_CASE("RugnuxCommandLine_AzInt", "[process]") {

tests/SearchSpaceGroupTest.cpp

@@ -150,7 +150,7 @@ TEST_CASE("SearchSpaceGroup detects synthetic space groups") {
 
 // Regression: a real screw axis whose systematically-absent reflections carry a genuinely weak
 // intensity but an UNDER-estimated sigma (so their I/sigma clears the "present" cut) must still be
-// found. Reproduces the monoclinic 2_1 miss on EP_cs_02-10 / EP_cs_01-17, where the merged sigmas on
+// found. Reproduces a monoclinic 2_1 miss on weakly-diffracting monoclinic data, where the merged sigmas on
 // the 0k0-odd reflections were ~2x too small and faked screw-axis violations. The E^2 intensity gate
 // (present_e_squared) is what keeps those reflections classified absent.
 TEST_CASE("SearchSpaceGroup finds a screw axis despite under-estimated sigmas on absent reflections") {

tests/XtalOptimizerTest.cpp

@@ -538,10 +538,14 @@ TEST_CASE("XtalOptimizer_rotation") {
         }
     }
 
-    // Seed slightly perturbed geometry and lattice; provide rotation axis for refinement
+    // Seed slightly perturbed geometry and lattice; provide rotation axis for refinement.
+    // The beam-centre component PARALLEL to the spindle (here X, the rotation axis) is a gauge-weak
+    // direction that XtalOptimizer now deliberately restrains toward the header rather than refining
+    // freely (see the BeamComponentPrior in XtalOptimizer.cpp). So only the perpendicular component
+    // (Y) is seeded off-truth to exercise beam-centre recovery; X is seeded at its true value.
     XtalOptimizerData xtal_opt{};
     xtal_opt.latt = CrystalLattice(39.7f, 50.6f, 79.6f, 90.0f, 94.5f, 90.5f);
-    xtal_opt.geom.BeamX_pxl(1003).BeamY_pxl(997).DetectorDistance_mm(203.0)
+    xtal_opt.geom.BeamX_pxl(1000).BeamY_pxl(997).DetectorDistance_mm(203.0)
             .PoniRot1_rad(0.01).PoniRot2_rad(0.02);
     xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
     xtal_opt.axis = axis;

tests/ZSTDCompressorTest.cpp

@@ -366,7 +366,7 @@ TEST_CASE("ZstdHuff_MaskLike", "[ZSTD]") {
     RequireHuffRoundTrip(image);
 }
 
-TEST_CASE("ZstdHuff_LysoImage", "[ZSTD]") {
+TEST_CASE("ZstdHuff_BenchmarkImage", "[ZSTD]") {
     RegisterHDF5Filter();   // bitshuffle filter, needed to read the compressed benchmark dataset
     HDF5ReadOnlyFile data("../../tests/test_data/compression_benchmark.h5");
     HDF5DataSet dataset(data, "/entry/data/data");

tests/crystfel/README.md

@@ -17,7 +17,7 @@ Go back to main directory and:
 cd crystfel
 HDF5DATASET_WRITE_TEST_SWMR=1 ../build/tests/HDF5DatasetWriteTest ../tests/test_data/compression_benchmark.h5 100
 ```
-This will generate HDF5 with lysozyme data measured with JUNGFRAU 4 Mpixel long time ago.
+This will generate HDF5 with protein diffraction data measured with JUNGFRAU 4 Mpixel long time ago.
 
 ## Analyze with CrystFEL
 To process the generated file with CrystFEL, you need to run the following command:
@@ -30,5 +30,5 @@ Final: 100 images processed, 100 hits (100.0%), 100 indexable (100.0% of hits, 1
 ```
 In case of issues, you can also try providing unit cell information:
 ```
-indexamajig -g jf4m.geom -i writing_test.lst -o writing_test.stream --indexing=xgandalf -p 6G8A.pdb
+indexamajig -g jf4m.geom -i writing_test.lst -o writing_test.stream --indexing=xgandalf -p cell.pdb
 ```

tests/crystfel/cell.pdb

@@ -0,0 +1,4 @@
+REMARK  Unit-cell reference for the optional CrystFEL indexing hint (see README.md).
+REMARK  Contains only the cell of the benchmark diffraction data - no model.
+CRYST1   78.903   78.903   36.941  90.00  90.00  90.00 P 43 21 2     8
+END

tests/data/README.md

@@ -20,10 +20,10 @@ git lfs pull            # or: git lfs pull --include "tests/data/*.h5"
 
 | File                       | Dataset                                 | Shipped   |
 |----------------------------|-----------------------------------------|-----------|
-| `lyso_rotation_master.h5`  | lysozyme rotation series (~1800 images) | yes (LFS) |
+| `rotation_master.h5`       | protein rotation series (~1800 images)  | yes (LFS) |
 
-`lyso_rotation_master.h5` (plus its `_data_NNNNNN.h5` files) is fetched by `git lfs pull` and
-drives `Rugnux_LysoRotation`. A separate serial dataset is intentionally **not** shipped
+`rotation_master.h5` (plus its `_data_NNNNNN.h5` files) is fetched by `git lfs pull` and
+drives `Rugnux_Rotation`. A separate serial dataset is intentionally **not** shipped
 to keep the repository small — the rotation series can be run in serial mode (full analysis
 without rotation indexing) to exercise that path. To add your own dataset, drop the master + its
 data files here as real files (not symlinks, if you intend to commit them via LFS); the master

tests/test_data/jfjoch_broker_test.py

@@ -17,10 +17,10 @@ start_input = {
     "beam_y_pxl":1136,
     "detector_distance_mm":75, 
     "incident_energy_keV":12.4,
-    "sample_name":"lyso", 
+    "sample_name":"test_sample",
     "unit_cell":{"a":36.9, "b":78.95, "c":78.95, "alpha":90, "beta":90, "gamma":90}, 
     "images_per_trigger":18,
-    "file_prefix":"lyso_test_grid",
+    "file_prefix":"test_grid",
     "grid_scan": {
 	"n_fast":3,
         "step_x_um": 5.0,