v1.0.0-rc.131 (#39)

This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124.

* jfjoch_broker: Fix bug in saving JUNGFRAU calibration (pedestal/pedestalRMS)
* jfjoch_viewer: Fix calibration (pedestal) images being open flipped
* jfjoch_process: Add space group detection (EXPERIMENTAL)

Reviewed-on: #39

tests/SearchSpaceGroupTest.cpp

@@ -0,0 +1,150 @@
+#include <catch2/catch_all.hpp>
+
+#include "../image_analysis/scale_merge/SearchSpaceGroup.h"
+#include "gemmi/symmetry.hpp"
+
+#include <cmath>
+#include <cstdint>
+#include <string>
+#include <tuple>
+#include <unordered_set>
+#include <vector>
+
+namespace {
+    struct HKL {
+        int h = 0;
+        int k = 0;
+        int l = 0;
+
+        bool operator==(const HKL& o) const noexcept {
+            return h == o.h && k == o.k && l == o.l;
+        }
+    };
+
+    struct HKLHash {
+        size_t operator()(const HKL& x) const noexcept {
+            auto mix = [](uint64_t v) {
+                v ^= v >> 33;
+                v *= 0xff51afd7ed558ccdULL;
+                v ^= v >> 33;
+                v *= 0xc4ceb9fe1a85ec53ULL;
+                v ^= v >> 33;
+                return v;
+            };
+            return static_cast<size_t>(
+                mix(static_cast<uint64_t>(x.h)) ^
+                (mix(static_cast<uint64_t>(x.k)) << 1) ^
+                (mix(static_cast<uint64_t>(x.l)) << 2));
+        }
+    };
+
+    double CalcSyntheticD(int h, int k, int l) {
+        const double q2 = static_cast<double>(h * h + k * k + l * l);
+        return 40.0 / std::sqrt(q2 + 1.0);
+    }
+
+    double SyntheticIntensityFromAsu(const gemmi::Op::Miller& asu) {
+        uint64_t x = static_cast<uint64_t>((asu[0] + 31) * 73856093u) ^
+                     static_cast<uint64_t>((asu[1] + 37) * 19349663u) ^
+                     static_cast<uint64_t>((asu[2] + 41) * 83492791u);
+        x ^= x >> 13;
+        x *= 0x9e3779b97f4a7c15ULL;
+        x ^= x >> 17;
+        return 100.0 + static_cast<double>(x % 500);
+    }
+
+    std::vector<MergedReflection> GenerateMergedReflectionsForSpaceGroup(
+        const gemmi::SpaceGroup& sg,
+        int hmax = 8) {
+
+        std::vector<MergedReflection> merged;
+        std::unordered_set<HKL, HKLHash> added;
+
+        const gemmi::GroupOps gops = sg.operations();
+        const gemmi::ReciprocalAsu rasu(&sg);
+
+        for (int h = -hmax; h <= hmax; ++h) {
+            for (int k = -hmax; k <= hmax; ++k) {
+                for (int l = -hmax; l <= hmax; ++l) {
+                    if (h == 0 && k == 0 && l == 0)
+                        continue;
+
+                    bool absent = false;
+                    gemmi::Op::Miller hkl{{h, k, l}};
+                    if (gops.is_systematically_absent(hkl))
+                        absent = true;
+
+                    const auto [asu, sign_plus] = rasu.to_asu_sign(hkl, gops);
+                    if (!sign_plus)
+                        continue;
+
+                    const HKL key{h, k, l};
+                    if (added.find(key) != added.end())
+                        continue;
+                    added.insert(key);
+
+                    merged.push_back(MergedReflection{
+                        .h = h,
+                        .k = k,
+                        .l = l,
+                        .I = absent ? 0.0 : SyntheticIntensityFromAsu(asu),
+                        .sigma = 1.0,
+                        .d = CalcSyntheticD(h, k, l)
+                    });
+                }
+            }
+        }
+
+        return merged;
+    }
+}
+
+TEST_CASE("SearchSpaceGroup detects synthetic space groups") {
+    struct Case {
+        std::string input_name;
+        std::string expected_short_name;
+    };
+
+    const std::vector<Case> cases = {
+        {"P 1", "P1"},
+        {"P 1 2 1", "P2"},
+        {"P 3 2 1", "P321"},
+        {"P 4 2 2", "P422"},
+        {"P 4 3 2", "P432"},
+        {"P 43 21 2", "P43212"},
+        {"P 6 2 2", "P622"},
+        {"C 1 2 1", "C2"},
+        {"C 2 2 2", "C222"},
+        {"I 4 3 2", "I432"},
+        {"I 21 21 21", "I212121"},
+        {"I 2 1 3", "I213"},
+    };
+
+    for (const auto& tc : cases) {
+        DYNAMIC_SECTION(tc.expected_short_name) {
+            const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name(tc.input_name);
+            const auto merged = GenerateMergedReflectionsForSpaceGroup(sg);
+
+            SearchSpaceGroupOptions opt;
+            opt.crystal_system.reset();
+            opt.centering = '\0';
+            opt.merge_friedel = true;
+            opt.d_min_limit_A = 2.0;
+            opt.min_operator_cc = 0.99;
+            opt.min_pairs_per_operator = 20;
+            opt.min_total_compared = 80;
+            opt.test_systematic_absences = true;
+            opt.absence_resolution_bins = 10;
+            opt.min_absent_reflections_per_bin = 5;
+            opt.min_allowed_reflections_per_bin = 10;
+            opt.max_absent_to_allowed_i_over_sigma_ratio = 0.05;
+            opt.max_absent_to_allowed_i_over_sigma_ratio_in_any_bin = 0.10;
+
+            const auto result = SearchSpaceGroup(merged, opt);
+
+            INFO(SearchSpaceGroupResultToText(result));
+            REQUIRE(result.best_space_group.has_value());
+            CHECK(result.best_space_group->short_name() == tc.expected_short_name);
+        }
+    }
+}