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>

common/PixelMask.cpp

@@ -59,6 +59,9 @@ void PixelMask::UpdateBinaryMask() {
     for (size_t i = 0; i < mask.size(); i++)
         binary_mask[i] = (mask[i] != 0);
     binary_mask_checksum = TableChecksum(binary_mask.data(), binary_mask.size());
+    packed_mask.assign((mask.size() + 31) / 32, 0);
+    for (size_t i = 0; i < mask.size(); i++)
+        packed_mask[i / 32] |= static_cast<uint32_t>(binary_mask[i]) << (i % 32);
 }
 
 void PixelMask::CalcEdgePixels_i(const DiffractionExperiment &experiment) {
@@ -127,6 +130,10 @@ const std::vector<uint8_t> &PixelMask::GetBinaryMask() const {
     return binary_mask;
 }
 
+const std::vector<uint32_t> &PixelMask::GetPackedMask() const {
+    return packed_mask;
+}
+
 uint64_t PixelMask::GetBinaryMaskChecksum() const {
     return binary_mask_checksum;
 }
@@ -247,6 +254,14 @@ void PixelMask::LoadBeamStopMask(const DiffractionExperiment& experiment, const
     UpdateDerived(experiment);
 }
 
+void PixelMask::LoadHotPixelMask(const DiffractionExperiment& experiment, const std::vector<uint32_t> &in_mask) {
+    if (in_mask.size() != mask.size())
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Size of input hot pixel mask invalid");
+    LoadMask(in_mask, HotPixelBit);
+    UpdateDerived(experiment);
+}
+
 void PixelMask::ClearBeamStopMask(const DiffractionExperiment& experiment) {
     for (auto &i: mask)
         i &= ~(1u << BeamStopPixelBit);