JFJochHDF5Reader: Use lattice, and not Niggli class, to decode symmetry (if symmetry is imposed, then lattice search returns niggli class 0

tests/JFJochReaderTest.cpp

@@ -1038,6 +1038,79 @@ TEST_CASE("JFJochReader_NiggliClass", "[HDF5][Full]") {
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
 
+TEST_CASE("JFJochReader_NiggliClass_VDS", "[HDF5][Full]") {
+    DiffractionExperiment x(DetJF(1));
+    x.FilePrefix("test95").ImagesPerTrigger(4).OverwriteExistingFiles(true);
+    x.BitDepthImage(16).ImagesPerFile(1).SetFileWriterFormat(FileWriterFormat::NXmxVDS).PixelSigned(true)
+            .IndexingAlgorithm(IndexingAlgorithmEnum::FFT);
+    x.Compression(CompressionAlgorithm::NO_COMPRESSION);
+
+    std::vector<int16_t> image(x.GetPixelsNum());
+
+    RegisterHDF5Filter();
+    {
+        StartMessage start_message;
+        x.FillMessage(start_message);
+        FileWriter file_set(start_message);
+
+        LatticeMessage lm{
+            .centering = 'F',
+            .niggli_class = 1,
+            .crystal_system = gemmi::CrystalSystem::Cubic,
+        };
+
+        DataMessage message{};
+        message.number = 0;
+        message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
+        message.indexing_result = true;
+        message.indexing_lattice = CrystalLattice(40, 50, 60, 90, 90, 90);
+        message.lattice_type = lm;
+        REQUIRE_NOTHROW(file_set.WriteHDF5(message));
+
+        message.number = 1;
+        message.indexing_result = false;
+        message.indexing_lattice = std::nullopt;
+        REQUIRE_NOTHROW(file_set.WriteHDF5(message));
+
+        EndMessage end_message;
+        end_message.max_image_number = 2;
+        file_set.WriteHDF5(end_message);
+        file_set.Finalize();
+    }
+    {
+        JFJochHDF5Reader reader;
+        REQUIRE_NOTHROW(reader.ReadFile("test95_master.h5"));
+        auto dataset = reader.GetDataset();
+        CHECK(dataset->experiment.GetImageNum() == 2);
+
+        std::shared_ptr<JFJochReaderImage> reader_image, reader_image_2;
+
+        REQUIRE_NOTHROW(reader_image = reader.LoadImage(0));
+
+        REQUIRE(reader_image);
+        CHECK(reader_image->ImageData().indexing_result.value() == true);
+        REQUIRE(reader_image->ImageData().indexing_lattice);
+        REQUIRE(reader_image->ImageData().lattice_type);
+        CHECK(reader_image->ImageData().lattice_type->centering == 'F');
+        CHECK(reader_image->ImageData().lattice_type->niggli_class == 1);
+        CHECK(reader_image->ImageData().lattice_type->crystal_system == gemmi::CrystalSystem::Cubic);
+
+        REQUIRE_NOTHROW(reader_image_2 = reader.LoadImage(1));
+
+        REQUIRE(reader_image_2);
+        CHECK(!reader_image_2->ImageData().indexing_result.value());
+        REQUIRE(!reader_image_2->ImageData().indexing_lattice);
+        REQUIRE(!reader_image_2->ImageData().lattice_type);
+    }
+    remove("test95_master.h5");
+    remove("test95_data_000001.h5");
+    remove("test95_data_000002.h5");
+
+    // No leftover HDF5 objects
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
+
 TEST_CASE("JFJochReader_MissingEntries", "[HDF5][Full]") {
     DiffractionExperiment x(DetJF(1));
     x.FilePrefix("test96").ImagesPerTrigger(4).OverwriteExistingFiles(true);