mx/Jungfraujoch
0
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases 37 Wiki Activity

jfjoch_viewer: Fix reading dataset with partial grid results

Browse Source
This commit is contained in:
leonarski_f
2025-11-21 17:54:15 +01:00
parent ddcc24fba8
commit 3602b634f8
3 changed files with 81 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
reader/JFJochHDF5Reader.cpp
View File

@@ -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) {}

82
tests/JFJochReaderTest.cpp
View File

@@ -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);
}
}

2
writer/HDF5Objects.h
View File

@@ -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)