reader/JFJochHDF5Reader.cpp

@@ -70,9 +70,9 @@ void JFJochHDF5Reader::ReadVector(std::vector<T> &v,
                                   size_t nimages) {
     try {
         auto tmp = file.ReadOptVector<T>(dataset_name);
-        if (tmp.size() == nimages) {
+        if (tmp.size() <= nimages) {
             v.resize(image0 + nimages);
-            for (int i = 0; i < nimages; i++)
+            for (int i = 0; i < tmp.size(); i++)
                 v[image0 + i] = tmp[i];
         }
     } catch (JFJochException &e) {}

tests/JFJochReaderTest.cpp

@@ -1050,9 +1050,83 @@ TEST_CASE("JFJochReader_NiggliClass", "[HDF5][Full]") {
         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");
+    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);
+    x.BitDepthImage(16).ImagesPerFile(10).SetFileWriterFormat(FileWriterFormat::NXmxLegacy).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);
+
+        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.spot_count_indexed = 56;
+        message.spot_count = 85;
+        message.b_factor = 123.45;
+        message.spots = {SpotToSave{.x = 10, .y=50, .intensity =  80}};
+        REQUIRE_NOTHROW(file_set.WriteHDF5(message));
+
+        message.number = 1;
+        message.indexing_result = false;
+        message.indexing_lattice = std::nullopt;
+        message.spot_count_indexed = std::nullopt;
+        message.spot_count = 70;
+        message.b_factor = std::nullopt;
+        message.spots = {SpotToSave{.x = 10, .y=50, .intensity =  80}};
+        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("test96_master.h5"));
+        auto dataset = reader.GetDataset();
+        CHECK(dataset->experiment.GetImageNum() == 2);
+
+        REQUIRE(dataset->b_factor.size() == 2);
+        REQUIRE(dataset->spot_count_indexed.size() == 2);
+
+        CHECK(dataset->b_factor[0] == Catch::Approx(123.45));
+        CHECK(dataset->b_factor[1] == 0.0);
+        CHECK(dataset->spot_count_indexed[0] == 56);
+        CHECK(dataset->spot_count_indexed[1] == 0);
+
+        std::shared_ptr<JFJochReaderImage> reader_image, reader_image_2;
+
+        REQUIRE_NOTHROW(reader_image = reader.LoadImage(0));
+        REQUIRE(reader_image);
+        REQUIRE(reader_image->ImageData().b_factor.has_value());
+        CHECK(reader_image->ImageData().b_factor.value() == Catch::Approx(123.45));
+        REQUIRE(reader_image->ImageData().spot_count_indexed.has_value());
+        CHECK(reader_image->ImageData().spot_count_indexed.value() == 56);
+
+        REQUIRE_NOTHROW(reader_image_2 = reader.LoadImage(1));
+        REQUIRE(reader_image_2);
+        CHECK(!reader_image_2->ImageData().spot_count_indexed);
+    }
+    remove("test96_master.h5");
+    remove("test96_data_000001.h5");
 
     // No leftover HDF5 objects
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
@@ -1318,4 +1392,4 @@ TEST_CASE("JFJochReader_InstrumentMetadata_Sample_RingCurrent", "[HDF5][Full]")
 
     remove("test_meta_master.h5");
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
-}
+}

writer/HDF5Objects.h

@@ -302,7 +302,7 @@ public:
         auto dims = file_space.GetDimensions();
         // Allow scalar (0-D) to be read with n==0 as a convenience.
         if (file_space.GetNumOfDimensions() == 0) {
-            if (n != 0) throw JFJochException(JFJochExceptionCategory::HDF5, "Index out of bounds for scalar dataset");
+            if (n != 0) return std::nullopt;
             return ReadScalar<T>();
         }
         if (file_space.GetNumOfDimensions() != 1)