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Record the corrections a DECTRIS detector applied; read multichannel NXmx

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The broker rebuilds the outgoing StartMessage from DiffractionExperiment,
and FillMessage hard-coded countrate_correction_enabled and
flatfield_enabled to false. JFJochReceiverLite parsed the true values from
the detector's stream2 start message and dropped them, so every DECTRIS
file written through the broker said neither correction was applied -
DECTRIS enables both by default. pixel_mask_applied had the same defect:
it reported the local apply_mask setting (an FPGA feature), not what the
detector did to the pixels, which ReceiverLite forwards byte for byte.

These now come from the stream: DetectorSetup carries them, ReceiverLite
copies them in Configure, FillMessage reads them. Two more fields the
DECTRIS stream sends and NXmx defines are passed through to the master
file: countrate_correction_lookup_table (uint32, possibly bslz4/bszstd
compressed in the stream) and virtual_pixel_interpolation_applied. The
flatfield is deliberately not written - it makes the master file too
large. PSI EIGER is unchanged: jfjoch never enables rate correction and
the detector server starts with it off.

The reader also opens the DECTRIS "hdf5 nexus v2024.2 nxmx" layout, where
/entry/data/data is 4D [image, channel, y, x] and the pixel mask is kept
per channel. Only the first channel is read; this is compatibility, not
full multichannel support. A _process.h5 made from such a file links its
pictures to that channel.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT
This commit is contained in:
leonarski_f
2026-09-23 21:04:16 +02:00
co-authored by Claude Opus 5.5
parent 0252880e06
commit aea13044b5
18 changed files with 397 additions and 31 deletions
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reader/HDF5MetadataSource.cpp
+17 -9
View File
@@ -153,9 +153,10 @@ inline std::pair<gemmi::CrystalSystem, char> parse_bravais_lattice(const std::st
return {cs, centering};
}
// [image, y, x], or [image, channel, y, x] as the DECTRIS "hdf5 nexus v2024.2 nxmx" format writes it
std::vector<hsize_t> GetDimension(HDF5Object &object, const std::string &path) {
const auto dim = object.GetDimension(path);
if (dim.size() != 3)
if (dim.size() != 3 && dim.size() != 4)
throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong dimension of " + path);
return dim;
}
@@ -174,9 +175,9 @@ std::vector<HDF5VirtualDatasetMapping> ReadVDSImageMappings(HDF5Object &file,
if (mapping.dataset.empty())
throw JFJochException(JFJochExceptionCategory::HDF5,
"VDS mapping has empty source dataset name");
if (mapping.virtual_start.size() != 3)
if (mapping.virtual_start.size() != 3 && mapping.virtual_start.size() != 4)
throw JFJochException(JFJochExceptionCategory::HDF5,
"Only 3D image VDS mappings are supported");
"Only 3D or 4D image VDS mappings are supported");
}
return mappings;
@@ -529,6 +530,8 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
size_t image_size_x = 0;
size_t image_size_y = 0;
// Of a multichannel master; only its first channel is read
std::string first_channel;
if (master_file->Exists("/entry/data/data")) {
HDF5DataSet data_dataset(*master_file, "/entry/data/data");
@@ -537,8 +540,10 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
auto dim = GetDimension(*master_file, "/entry/data/data");
number_of_images = dim[0];
image_size_y = dim[1];
image_size_x = dim[2];
image_size_y = dim[dim.size() - 2];
image_size_x = dim[dim.size() - 1];
if (dim.size() == 4)
first_channel = master_file->ReadElement<std::string>("/entry/data/channel", 0).value_or("");
images_per_file = number_of_images;
if (data_layout == HDF5DataSetLayout::VIRTUAL)
@@ -646,8 +651,8 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
const auto dim = GetDimension(data_file, data_path);
fimages = dim[0];
if (nfiles == 0) {
image_size_y = dim[1];
image_size_x = dim[2];
image_size_y = dim[dim.size() - 2];
image_size_x = dim[dim.size() - 1];
}
legacy_format_files.push_back({fname, data_path});
@@ -1112,8 +1117,11 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
// it, which a deposition shipping no mask at all leaves behind. The link is there, so
// the name exists; only opening it says whether the array does.
std::vector<uint32_t> mask_tmp;
for (const char *name: {"/entry/instrument/detector/pixel_mask",
"/entry/instrument/detector/detectorSpecific/pixel_mask"}) {
// A multichannel master keeps the mask per channel
const std::string channel_mask = "/entry/instrument/detector/" + first_channel + "_channel/pixel_mask";
for (const std::string &name: {channel_mask,
std::string("/entry/instrument/detector/pixel_mask"),
std::string("/entry/instrument/detector/detectorSpecific/pixel_mask")}) {
if (mask_tmp.empty() && master_file->IsDataSet(name))
mask_tmp = master_file->ReadVector<uint32_t>(name, {0, 0}, {image_size_y, image_size_x});
}