--prepass-fraction: the geometry pre-pass image loop on the first part of the sweep only

The two-pass rotation pipeline's first image loop (the geometry pre-pass whose reflections
feed post-refinement) stops after the given fraction of the sweep; pass 2 still integrates
every frame and is the only one written. Default 1 (unchanged).

On the 25 sets ranked by the post-refinement held-out gain, --prepass-fraction 0.5 vs rc174
(REFMAC check): 0 verdict changes, d_min change median 0.000, R-free worse by >0.005 on 1/17;
image-loop seconds -17%, myob wall 11.9 -> 10.5 s. Without post-refinement at all
(--rotation-no-postrefine) the same sets had 5 verdict changes and 11/17 R-free worse.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi

rugnux/Rugnux.cpp

@@ -6231,11 +6231,14 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
         AzimuthalIntegrationProfile profile(mapping);
         HarmonicEvidence worker_harmonic;
         std::vector<FootprintOffset> worker_offsets;
+        const int loop_end = geometry_prepass
+                ? start_image + static_cast<int>(std::lround((end_image - start_image) * config_.prepass_fraction))
+                : end_image;
 
         while (!cancelled_) {
             const int ordinal = next_ordinal.fetch_add(1);
             const int image_idx = start_image + ordinal * config_.stride;
-            if (image_idx >= end_image) break;
+            if (image_idx >= loop_end) break;
 
             // Reuse the raw image frame to frame - a fresh 4-byte 16 Mpx frame is 72 MB of
             // untouched pages the decoder faults in one by one - except while the writer thread

rugnux/Rugnux.h

@@ -100,6 +100,8 @@ struct ProcessConfig {
     bool rotation_indexing = false;
     bool two_pass_rotation = true;
     int rotation_indexing_image_count = 100;
+    // The geometry pre-pass image loop stops after this fraction of the sweep (pass 2 reads all of it).
+    double prepass_fraction = 1.0;
     std::optional<CrystalLattice> forced_rotation_lattice;
 
     // Stills global geometry-refinement two-pass (FullAnalysis, stills only). When set, an extra first

rugnux/rugnux_cli.cpp

@@ -142,6 +142,7 @@ void print_usage() {
     std::cout << "   --force-rotation-lattice <vec>   Force rotation indexer with external lattice (in Angstrom) : \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, skips first pass)" << std::endl;
     std::cout << "   --rotation-scale <k>             Goniometer rotation scale: the stage turned k times the angle stored in the file (the commanded one). Applied to both passes; overrides the fitted correction" << std::endl;
     std::cout << "   --rotation-no-postrefine         Disable the (default-on) two-pass rotation post-refine (post-refine detector distance/beam + cell/axis, then re-integrate; only the refined pass is written, as the canonical <prefix>_* output)" << std::endl;
+    std::cout << "   --prepass-fraction <f>           Run the two-pass rotation geometry pre-pass on only the first fraction f of the sweep (0.05-1, default 1); pass 2 still reads every frame" << std::endl;
     std::cout << "   -X, --indexing-algorithm <txt>   Indexing algorithm (FFBIDX|FFT|FFTW|Auto|None)" << std::endl;
     std::cout << "   -S, --space-group <num|symbol>   Space group number (96) or symbol (P43212) - for indexing and scaling" << std::endl;
     std::cout << "   -C, --unit-cell <cell>           Fix reference unit cell: \"a,b,c,alpha,beta,gamma\"" << std::endl;
@@ -249,6 +250,7 @@ enum {
     OPT_FORCE_ROTATION_LATTICE,
     OPT_MIN_INDEXED_SPOTS,
     OPT_ROTATION_NO_POSTREFINE,
+    OPT_PREPASS_FRACTION,
     OPT_ROTATION_SCALE,
     OPT_BACKGROUND_CLIP,
     OPT_BACKGROUND_RADIAL,
@@ -380,6 +382,7 @@ static option long_options[] = {
     {"polarization", required_argument, nullptr, OPT_POLARIZATION},
     {"force-rotation-lattice", required_argument, nullptr, OPT_FORCE_ROTATION_LATTICE},
     {"rotation-no-postrefine", no_argument, nullptr, OPT_ROTATION_NO_POSTREFINE},
+    {"prepass-fraction", required_argument, nullptr, OPT_PREPASS_FRACTION},
     {"rotation-scale", required_argument, nullptr, OPT_ROTATION_SCALE},
     {"refine-geometry", optional_argument, nullptr, OPT_REFINE_GEOMETRY},
     {"detect-beam-stop", optional_argument, nullptr, OPT_DETECT_BEAM_STOP},
@@ -752,6 +755,7 @@ static int RunRugnux(int argc, char **argv) {
     bool rotation_postrefine_geometry = true;   // default on; --rotation-no-postrefine disables it
     std::optional<float> rotation_scale;        // --rotation-scale: asserted stage calibration
     int rotation_indexing_image_count = 100;
+    double prepass_fraction = 1.0;
     std::optional<float> rotation_indexing_range;
     std::optional<int64_t> min_indexed_spots;   // --min-indexed-spots: spots on the lattice for a frame to count as indexed
     bool run_scaling = true;      // merge is on by default; --no-merge turns it off
@@ -894,6 +898,9 @@ static int RunRugnux(int argc, char **argv) {
         case OPT_ROTATION_NO_POSTREFINE:
             rotation_postrefine_geometry = false;
             break;
+        case OPT_PREPASS_FRACTION:
+            prepass_fraction = parse_number_arg<double>(optarg, "--prepass-fraction", logger, 0.05, 1.0);
+            break;
         case OPT_ROTATION_SCALE:
             rotation_scale = parse_number_arg<float>(optarg, "--rotation-scale", logger, 0.9f, 1.1f);
             break;
@@ -2813,6 +2820,7 @@ static int RunRugnux(int argc, char **argv) {
     config.measure_spot_budget = !max_spot_count_override.has_value();
     config.rotation_scale = rotation_scale;
     config.rotation_indexing_image_count = rotation_indexing_image_count;
+    config.prepass_fraction = prepass_fraction;
     config.forced_rotation_lattice = forced_rotation_lattice;
     config.refine_geometry = refine_geometry;
     config.run_scaling = run_scaling;