v1.0.0-rc.173 (#83)

* jfjoch_broker: Optional per-dataset authentication - statistics, images and plots can require a bearer token, which jfjoch_viewer supports.
* jfjoch_viewer: Dark mode and a theme-matched colour scheme, a magnifier panel, and simpler contrast and background controls.
* Rugnux: Multiple performance improvements on GPU and CPU (CPU-only processing up to 40% faster, faster image decoding on ARM), with unchanged results.
* Rugnux: `--model` rigid-body refinement runs on the GPU, and the model-validation check is faster and more reliable.
* Rugnux: Improved scaling and merging - error model, outlier rejection, absorption correction and French-Wilson amplitudes now agree more closely with XDS and ctruncate.
* Rugnux: Improved integration - radial background on powder and ice rings, crowded rotation data keep their reflections, and CPU-only builds integrate large unit cells as GPU builds do.
* Rugnux: More robust detector geometry - measured beam centre, X-ray bandwidth and goniometer rate, and geometry refinement accepted only on significant evidence.
* Rugnux: Merged files are written in the standard setting, or in the setting of a reference MTZ, structure-factor mmCIF or model, with its free-R flags.
* Rugnux: Richer report - ice and powder rings, further lattices, superstructure candidates and mosaicity, with warnings worded as prompts to check.
* Rugnux: Clear error messages when a data set needs more GPU or host memory than is available.

Reviewed-on: #83
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

reader/HDF5MetadataSource.cpp

@@ -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});
             }