v1.0.0-rc.156 (#66)

This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.

* jfjoch_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output.
* jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling.
* Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool.
* jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection.
* jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata.
* CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

image_analysis/WriteReflections.cpp

@@ -2,6 +2,7 @@
 // SPDX-License-Identifier: GPL-3.0-only
 
 #include "WriteReflections.h"
+#include "scale_merge/Merge.h"
 
 #include <cmath>
 #include <fstream>
@@ -59,6 +60,8 @@ std::string CifStr(const std::string& s) {
 void WriteMmcifReflections(const std::vector<MergedReflection> &reflections,
                            const UnitCell &unitCell,
                            const DiffractionExperiment &experiment,
+                           const MergeStatistics &statistics,
+                           const std::string &isa,
                            const std::string &filename) {
 
     std::ofstream out(filename);
@@ -110,6 +113,51 @@ void WriteMmcifReflections(const std::vector<MergedReflection> &reflections,
 
     out << "_diffrn_radiation_wavelength.wavelength  " << Fmt(experiment.GetWavelength_A(), 5) << "\n";
     out << "_diffrn_detector.detector  " << CifStr(experiment.GetDetectorDescription()) << "\n";
+    out << "#\n";
+
+    // ---------- merging statistics (_reflns overall + _reflns_shell loop) ----------
+    // cc_half and r_meas are stored as fractions (0-1), which is the mmCIF convention. ISa (the
+    // Diederichs asymptotic I/sigma, 1/b of the a*sigma^2 + (b*I)^2 error model) has no standard CIF
+    // item, so it is written as a free-text pdbx value.
+    const auto mult = [](const MergeStatisticsShell &s) {
+        return s.unique_reflections > 0 ? static_cast<double>(s.total_observations) / s.unique_reflections : 0.0; };
+    const auto compl_pct = [](const MergeStatisticsShell &s) {
+        return s.possible_unique_reflections > 0
+               ? 100.0 * static_cast<double>(s.unique_reflections) / s.possible_unique_reflections : 0.0; };
+    if (!statistics.shells.empty()) {
+        const auto &ov = statistics.overall;
+        out << "_reflns.d_resolution_high         " << Fmt(ov.d_min, 2) << "\n";
+        out << "_reflns.d_resolution_low          " << Fmt(ov.d_max, 2) << "\n";
+        out << "_reflns.number_obs                " << ov.unique_reflections << "\n";
+        out << "_reflns.pdbx_number_measured_all  " << ov.total_observations << "\n";
+        out << "_reflns.pdbx_redundancy           " << Fmt(mult(ov), 2) << "\n";
+        out << "_reflns.percent_possible_obs      " << Fmt(compl_pct(ov), 1) << "\n";
+        out << "_reflns.pdbx_netI_over_sigmaI     " << Fmt(ov.mean_i_over_sigma, 2) << "\n";
+        out << "_reflns.pdbx_Rrim_I_all           " << Fmt(ov.r_meas, 4) << "\n";
+        out << "_reflns.pdbx_CC_half              " << Fmt(ov.cc_half, 4) << "\n";
+        out << "_reflns.pdbx_diffrn_ISa           " << CifStr(isa) << "   # asymptotic I/sigma (Diederichs)\n";
+        out << "#\n";
+
+        out << "loop_\n";
+        out << "_reflns_shell.d_res_high\n";
+        out << "_reflns_shell.d_res_low\n";
+        out << "_reflns_shell.number_measured_obs\n";
+        out << "_reflns_shell.number_unique_obs\n";
+        out << "_reflns_shell.pdbx_redundancy\n";
+        out << "_reflns_shell.percent_possible_obs\n";
+        out << "_reflns_shell.meanI_over_sigI_obs\n";
+        out << "_reflns_shell.pdbx_Rrim_I_all\n";
+        out << "_reflns_shell.pdbx_CC_half\n";
+        for (const auto &s : statistics.shells) {
+            if (s.unique_reflections == 0)
+                continue;
+            out << Fmt(s.d_min, 2) << " " << Fmt(s.d_max, 2) << " "
+                << s.total_observations << " " << s.unique_reflections << " "
+                << Fmt(mult(s), 2) << " " << Fmt(compl_pct(s), 1) << " "
+                << Fmt(s.mean_i_over_sigma, 2) << " " << Fmt(s.r_meas, 4) << " " << Fmt(s.cc_half, 4) << "\n";
+        }
+        out << "#\n";
+    }
 
     // ---------- _refln loop ----------
     out << "loop_\n";
@@ -199,13 +247,15 @@ void WriteHKLReflections(const std::vector<MergedReflection> &reflections,
 void WriteReflections(const std::vector<MergedReflection> &reflections,
                       const UnitCell &unitCell,
                       const DiffractionExperiment &experiment,
+                      const MergeStatistics &statistics,
+                      const std::string &isa,
                       const std::string &filename) {
     switch (experiment.GetScalingSettings().GetFileFormat()) {
         case IntensityFormat::Text:
             WriteHKLReflections(reflections, filename + ".hkl");
             break;
         case IntensityFormat::mmCIF:
-            WriteMmcifReflections(reflections, unitCell, experiment, filename + ".cif");
+            WriteMmcifReflections(reflections, unitCell, experiment, statistics, isa, filename + ".cif");
             break;
         case IntensityFormat::MTZ:
             WriteMtzReflections(reflections, unitCell, experiment, filename + ".mtz");