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>

tests/SearchSpaceGroupTest.cpp

@@ -3,6 +3,7 @@
 #include "../image_analysis/scale_merge/SearchSpaceGroup.h"
 #include "gemmi/symmetry.hpp"
 
+#include <algorithm>
 #include <cmath>
 #include <cstdint>
 #include <string>
@@ -126,25 +127,67 @@ TEST_CASE("SearchSpaceGroup detects synthetic space groups") {
             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);
 
+            // Several inputs cannot be told apart from intensities alone: enantiomorphic partners
+            // (P4_3 vs P4_1) and origin-ambiguous pairs (I2_12_12_1 vs I222, I2_13 vs I2_3) share
+            // the same systematic absences. The search reports those as alternatives, so the
+            // expected group must appear among the best group and its alternatives.
+            std::vector<std::string> accepted;
+            if (result.best_space_group.has_value())
+                accepted.push_back(result.best_space_group->short_name());
+            for (const auto& alt : result.alternatives)
+                accepted.push_back(alt.short_name());
+
             INFO(SearchSpaceGroupResultToText(result));
             REQUIRE(result.best_space_group.has_value());
-            CHECK(result.best_space_group->short_name() == tc.expected_short_name);
+            CHECK(std::find(accepted.begin(), accepted.end(), tc.expected_short_name) != accepted.end());
         }
     }
+}
+
+// Regression: a real screw axis whose systematically-absent reflections carry a genuinely weak
+// intensity but an UNDER-estimated sigma (so their I/sigma clears the "present" cut) must still be
+// found. Reproduces the monoclinic 2_1 miss on EP_cs_02-10 / EP_cs_01-17, where the merged sigmas on
+// the 0k0-odd reflections were ~2x too small and faked screw-axis violations. The E^2 intensity gate
+// (present_e_squared) is what keeps those reflections classified absent.
+TEST_CASE("SearchSpaceGroup finds a screw axis despite under-estimated sigmas on absent reflections") {
+    const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("P 1 21 1");
+    auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 18);
+
+    // Every systematically-absent (0k0, k odd) reflection: small-but-nonzero intensity (~2% of a
+    // normal reflection) with a far-too-small sigma, so I/sigma ~ 27 fakes a "present" reflection.
+    const gemmi::GroupOps gops = sg.operations();
+    int absent_count = 0;
+    for (auto& r : merged) {
+        const gemmi::Op::Miller hkl{{r.h, r.k, r.l}};
+        if (gops.is_systematically_absent(hkl)) {
+            r.I = 8.0f;
+            r.sigma = 0.3f;
+            ++absent_count;
+        }
+    }
+    REQUIRE(absent_count >= 8);   // enough predicted-absent reflections to be trusted
+
+    SearchSpaceGroupOptions opt;
+    opt.merge_friedel = true;
+
+    SECTION("intensity gate on (default): screw recovered") {
+        const auto result = SearchSpaceGroup(merged, opt);
+        INFO(SearchSpaceGroupResultToText(result));
+        REQUIRE(result.best_space_group.has_value());
+        CHECK(result.best_space_group->short_name() == "P21");
+    }
+
+    SECTION("intensity gate off (I/sigma only): the screw is missed") {
+        // Documents the failure the gate fixes: with I/sigma alone the too-small sigmas fake
+        // violations and the search falls back to the symmorphic group.
+        opt.present_e_squared = 0.0;
+        const auto result = SearchSpaceGroup(merged, opt);
+        INFO(SearchSpaceGroupResultToText(result));
+        REQUIRE(result.best_space_group.has_value());
+        CHECK(result.best_space_group->short_name() == "P2");
+    }
 }