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/HDF5ImageLocator.cpp

@@ -12,7 +12,8 @@ namespace {
                                      const std::string &dataset,
                                      uint64_t source_first_image,
                                      uint64_t virtual_first_image,
-                                     uint64_t image_count) {
+                                     uint64_t image_count,
+                                     std::optional<uint64_t> source_channel = {}) {
         if (image_count == 0)
             return;
 
@@ -20,6 +21,7 @@ namespace {
             auto &last = ret.back();
             if (last.filename == filename
                 && last.dataset == dataset
+                && last.source_channel == source_channel
                 && last.source_first_image + last.image_count == source_first_image
                 && last.virtual_first_image + last.image_count == virtual_first_image) {
                 last.image_count += image_count;
@@ -32,9 +34,22 @@ namespace {
             .dataset = dataset,
             .source_first_image = source_first_image,
             .virtual_first_image = virtual_first_image,
-            .image_count = image_count
+            .image_count = image_count,
+            .source_channel = source_channel
         });
     }
+
+    // A 4D mapping, [image, channel, y, x], may cover only some of the channels; the reader wants
+    // the first one.
+    bool CoversFirstChannel(const HDF5VirtualDatasetMapping &mapping) {
+        return mapping.virtual_start.size() != 4 || mapping.virtual_start[1] == 0;
+    }
+
+    std::optional<hsize_t> SourceChannel(const HDF5VirtualDatasetMapping &mapping) {
+        if (mapping.source_start.size() == 4)
+            return mapping.source_start[1];
+        return {};
+    }
 }
 
 void HDF5ImageLocator::Configure(Layout layout) {
@@ -71,10 +86,10 @@ HDF5ImageLocator::Location HDF5ImageLocator::Resolve(int64_t global_image) const
         && layout_.data_layout == HDF5DataSetLayout::VIRTUAL) {
         const auto image = static_cast<hsize_t>(global_image);
         for (const auto &mapping: layout_.vds_mappings) {
-            if (!mapping.ContainsVirtualImage(image))
+            if (!CoversFirstChannel(mapping) || !mapping.ContainsVirtualImage(image))
                 continue;
             return {OpenCached(mapping.filename), static_cast<uint32_t>(mapping.SourceImage(image)),
-                    mapping.filename, mapping.dataset};
+                    mapping.filename, mapping.dataset, SourceChannel(mapping).value_or(0)};
         }
         throw JFJochException(JFJochExceptionCategory::HDF5,
                               "Image not covered by /entry/data/data VDS mappings");
@@ -127,13 +142,14 @@ std::vector<HDF5DataSourceMessage> HDF5ImageLocator::GetSourceMapping(uint64_t f
 
             bool found = false;
             for (const auto &mapping: layout_.vds_mappings) {
-                if (!mapping.ContainsVirtualImage(virtual_image))
+                if (!CoversFirstChannel(mapping) || !mapping.ContainsVirtualImage(virtual_image))
                     continue;
 
                 const uint64_t source_image = mapping.SourceImage(virtual_image);
                 const std::string dataset = mapping.dataset.empty() ? "/entry/data/data" : mapping.dataset;
 
-                AppendOrExtendSourceMapping(ret, mapping.filename, dataset, source_image, local_image, 1);
+                AppendOrExtendSourceMapping(ret, mapping.filename, dataset, source_image, local_image, 1,
+                                            SourceChannel(mapping));
                 found = true;
                 break;
             }