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/HDF5ImageSource.cpp

@@ -4,6 +4,8 @@
 #include "HDF5ImageSource.h"
 #include "../common/JFJochException.h"
 
+#include <algorithm>
+
 #ifdef _WIN32
 #include <windows.h>
 #else
@@ -97,22 +99,26 @@ HDF5ImageSource::GetDataset(const HDF5ImageLocator::Location &loc) const {
     HDF5DataType datatype(*entry.dataset);
     HDF5Dcpl dcpl(*entry.dataset);
 
-    if (dataspace.GetNumOfDimensions() != 3)
+    const auto rank = dataspace.GetNumOfDimensions();
+    if (rank != 3 && rank != 4)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              loc.dataset + " dataset must be 3D");
+                              loc.dataset + " dataset must be 3D or 4D");
+    entry.multichannel = (rank == 4);
 
     if (datatype.IsFloat())
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Float datasets not supported at this time");
 
     auto dim = dataspace.GetDimensions();
-    entry.height = dim[1];
-    entry.width = dim[2];
+    entry.height = dim[rank - 2];
+    entry.width = dim[rank - 1];
     entry.mode = CalcImageMode(datatype.GetElemSize(), datatype.IsFloat(), datatype.IsSigned());
 
+    // One chunk per image: [1, h, w], or [1, 1, h, w] for a multichannel dataset
     auto chunk_size = dcpl.GetChunking();
-    entry.direct_chunk = (chunk_size.size() == 3) && (chunk_size[0] == 1)
-                         && (chunk_size[1] == dim[1]) && (chunk_size[2] == dim[2]);
+    entry.direct_chunk = (chunk_size.size() == rank)
+                         && std::all_of(chunk_size.begin(), chunk_size.end() - 2, [](hsize_t c) { return c == 1; })
+                         && (chunk_size[rank - 2] == entry.height) && (chunk_size[rank - 1] == entry.width);
     if (entry.direct_chunk)
         entry.algorithm = dcpl.GetCompression();
 
@@ -155,7 +161,9 @@ HDF5ImageSource::PrepareDirectRead(const HDF5ImageLocator::Location &loc) const
     if (!ds.raw)
         return {};
 
-    const hsize_t coord[3] = {static_cast<hsize_t>(loc.local_index), 0, 0};
+    const hsize_t coord_3d[3] = {loc.local_index, 0, 0};
+    const hsize_t coord_4d[4] = {loc.local_index, loc.channel, 0, 0};
+    const hsize_t *coord = ds.multichannel ? coord_4d : coord_3d;
     unsigned filter_mask = 0;
     haddr_t address = HADDR_UNDEF;
     hsize_t size = 0;