rugnux: the geometry refinement algorithm is -r, --geom-refine; --refine was declared twice and its no-argument form shadowed it

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu

docs/RUGNUX_ADVANCED.md

@@ -427,7 +427,7 @@ For very long axes the direction grid's angular resolution binds well below 500
 | `--fft-min-unit-cell <num>` | Shortest cell axis the FFT search accepts, Å (default: 10). A candidate with a shorter axis is discarded — but a de-novo rotation run also runs a **second first-pass hypothesis with the floor lowered to 5 Å by default**, adopted when the standing cell turns out to be an integer supercell of what it finds, so a small-molecule cell is indexed without this flag. `-C` lowers the floor on its own to cover the cell given (and the second hypothesis then stays out of the way). On stills, where neither applies, a crystal below the floor cannot be indexed unless this is lowered |
 | `--min-indexed-spots <num>` | Spots a frame must have on the lattice before it counts as indexed (default: 6, minimum 4). It sets the reported indexing rate and the count the rotation first pass ranks candidate lattices by; whether the run has a lattice at all is decided on the pooled spots instead ([§4.1](CPU_DATA_ANALYSIS_INDEXING.md#41-indexed-spot-decision-inlier-test)), and integration is not gated by it |
 | `-S, --space-group <num\|symbol>` | Space group number (`96`) or Hermann-Mauguin symbol (`P43212`) — for indexing and scaling |
-| `-r, --refine <txt>` | Geometry refinement: `none` \| `orientation` \| `beam_and_lattice` (default) \| `flex` (try all three per image, keep whichever indexes the most spots; alias `multi`) |
+| `-r, --geom-refine <txt>` | Geometry refinement: `none` \| `orientation` \| `beam_and_lattice` (default) \| `flex` (try all three per image, keep whichever indexes the most spots; alias `multi`) |
 | `-R, --two-pass-rotation[=num]` | Two-pass offline rotation indexing (default for goniometer data; optional first-pass image count, default 100) |
 | `--single-pass-rotation[=num]` | Online-like single-pass rotation indexing (optional min angular range, deg) |
 | `--force-rotation-lattice <vec>` | Force rotation lattice (9 floats, Å), skipping the first pass |

rugnux/rugnux_cli.cpp

@@ -218,7 +218,7 @@ void print_usage() {
     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;
     std::cout << "   --fft-min-unit-cell <num>        Shortest cell axis the FFT search accepts, in A (default: 10). A candidate with a shorter axis is discarded, but a de-novo rotation run also tries a second first-pass hypothesis with the floor at 5 A, so a small-molecule cell is indexed without this flag; -C lowers it on its own to cover the cell given" << std::endl;
-    std::cout << "   -r, --refine <txt>               Geometry refinement algorithm (none|orientation|beam_and_lattice|flex); flex tries all three per image and keeps whichever indexes the most spots (alias: multi)" << std::endl;
+    std::cout << "   -r, --geom-refine <txt>          Geometry refinement algorithm (none|orientation|beam_and_lattice|flex); flex tries all three per image and keeps whichever indexes the most spots (alias: multi)" << std::endl;
     std::cout << "   --refine-geometry[=N|off]        Stills: extra first pass that bundle-adjusts the shared beam/distance/cell from N strongly-indexed frames (default: 200) then re-indexes (lifts weak-stills indexing). Default ON for stills when a reference cell is given (-C / reference MTZ); =off disables" << std::endl;
     std::cout << "   --refine-modules[=on|off|diagnose] Stills, in that bundle adjustment: a detector of several modules (the input's own - NXdetector_module groups, SACLA sensors, geometry-file panels - or --module-geometry) has each placed as a rigid block - shift and in-plane turn - where that predicts the spots better on frames held out of the fit (default: on). Used from there on for the panels of a foreign detector (SACLA sensors, geometry-file panels); for a JUNGFRAU measured and reported only. The placement is written to <prefix>_modules.h5" << std::endl;
     std::cout << "   --module-geometry <file>         Where the detector's modules are: an NXmx file with one NXdetector_module group per module (module_0, module_1, ...; what a run writes as <prefix>_modules.h5), or a CrystFEL geometry file whose panels are laid on the image (fs = column, ss = row). Replaces the input's own modules" << std::endl;
@@ -454,7 +454,7 @@ static option long_options[] = {
     {"relative-b", optional_argument, nullptr, OPT_RELATIVE_B},
     {"no-scaling-corrections", no_argument, nullptr, OPT_NO_SCALING_CORRECTIONS},
     {"no-expected-variance-merge", no_argument, nullptr, OPT_NO_EXPECTED_VARIANCE_MERGE},
-    {"refine", required_argument, nullptr, 'r'},
+    {"geom-refine", required_argument, nullptr, 'r'},
 
     {"two-pass-rotation", optional_argument, nullptr, 'R'},
     {"single-pass-rotation", optional_argument, nullptr, OPT_SINGLE_PASS_ROTATION},