v1.0.0-rc.178 (#88)

* Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`).
* Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels.
* Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL.
* jfjoch_viewer: Opens the same XFEL file formats.
* Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL.
* Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded.
* jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start.

Reviewed-on: #88
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

reader/HDF5MetadataSource.cpp

@@ -6,6 +6,7 @@
 #include <set>
 
 #include "HDF5MetadataSource.h"
+#include "NXmxModules.h"
 #include "spdlog/fmt/fmt.h"
 #include "../image_analysis/bragg_integration/CalcISigma.h"
 #include "../image_analysis/spot_finding/SpotUtils.h"
@@ -28,7 +29,9 @@ static Coord McStasToInternal(const std::vector<double> &v) {
 // separated from the tilt by looking at the module alone - so it is left as it is rather than
 // approximated. Every real file examined here is exactly discrete.
 static std::optional<DetectorOrientation> ReadModuleOrientation(HDF5Object *file) {
-    const std::string base = "/entry/instrument/detector/module/";
+    // One module for the whole image, or - where the file states its modules one by one - the first.
+    const std::string base = file->IsDataSet("/entry/instrument/detector/module/fast_pixel_direction")
+                             ? "/entry/instrument/detector/module/" : "/entry/instrument/detector/module_0/";
     if (!file->IsDataSet(base + "fast_pixel_direction") || !file->IsDataSet(base + "slow_pixel_direction"))
         return {};
 
@@ -1092,6 +1095,9 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
         detector.MinCountTime(std::chrono::microseconds(0));
         detector.ReadOutTime(std::chrono::nanoseconds(0));
         dataset->experiment.Detector(detector);
+        // The modules, where the file states them one by one (module_0, module_1, ...).
+        dataset->experiment.Modules(ReadNXmxModules(*master_file, detector.GetPixelSize_mm() / 1000.0,
+                                                    detector.GetImageOrientation()));
 
         // frame_time is the period between frames, count_time the exposure within one. NXmx requires
         // neither, and a master written outside the DECTRIS toolchain often carries only count_time;