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rugnux: keep 1000 spots per image instead of 250

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Offline reprocessing is not bound by the online spot budget, and the cap is
applied at the end of SpotAnalyze, so it is exactly the spot list the indexer
and the per-image refinement see. jfjoch_viewer already sends 1000, so the two
front ends now agree on the same file.

Measured as a paired A/B over the 37-crystal rotation battery, de novo, with the
resolution and Friedel setting matched to the XDS reference, both arms from the
same binary bar this constant:

  R_meas low shell   16 better    0 worse   19 unchanged
  R_meas             14 better    4 worse   17 unchanged
  ISa                14 better    6 worse   15 unchanged
  CC1/2               6 better    3 worse   26 unchanged

Low-resolution R_meas is a clean sweep. Around half the battery is bit-identical:
those frames never reach 250 spots, so the cap never bound. Wall clock is
unchanged (10m00s vs 10m44s, uncontrolled for page cache).

Known cost, and the reason this is its own commit: one crystal in the battery
reproducibly loses symmetry, tetragonal 422 -> orthorhombic 222, doubling its
asymmetric unit. Its R_meas and ISa "improve" there, but that is what merging in
too low a symmetry always does, and the lower symmetry then admits a merohedral
indexing ambiguity. An intermediate cap of 500 demotes it too, so it buys none of
the safety. This is the known point-group-decision-moves-with-data-amount
fragility of the space-group search rather than an argument for starving the
indexer of spots - the search is the thing to fix.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-08-03 22:08:21 +02:00
co-authored by Claude Opus 5
parent 2473e03cf7
commit f25fea7024
2 changed files with 12 additions and 5 deletions
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docs/RUGNUX.md
+1 -1
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@@ -210,7 +210,7 @@ Spot finding:
| `--spot-high-resolution <num>` | High-resolution limit for spot finding, Å. Omitted (or 0): no resolution clipping — spot finding extends as far as the detector reaches, for rotation data as well as stills |
| `--spot-low-resolution <num>` | Low-resolution limit for spot finding, Å (default: 50; lower it, e.g. 24, to exclude the direct-beam halo on weak serial data) |
| `--min-pix-per-spot <num>` | Minimum connected strong pixels per spot. **If omitted, min-pix is chosen per image** (stills indexing): the frame is indexed at min-pix 3/2/1 and the one maximising indexed-spot count × indexed fraction is kept. Give an explicit value to force a fixed min-pix instead. |
| `--max-spots <num>` | Maximum spot count (default: 250) |
| `--max-spots <num>` | Maximum spots kept per image (the strongest ones) and handed to indexing (default: 1000) |
| `--detect-ice-rings[=on\|off]` | Flag ice-ring spots (de-prioritised in indexing) and exclude ice-ring reflections from scaling/merging; overrides the dataset/master-file setting (default: use the dataset value) |
Azimuthal integration (the radial profile behind the per-image ice-ring score):
rugnux/rugnux_cli.cpp
+11 -4
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@@ -38,6 +38,14 @@
#include "RugnuxDefaults.h"
#include "ModelValidation.h"
// Spots kept per image (the strongest ones) and handed to indexing. Offline reprocessing is not
// bound by the online spot budget, so this is rugnux's own default rather than the 250 the
// DatasetSettings constructor uses for the detector. Measured over the 37-crystal rotation battery,
// lifting it to 1000 leaves low-resolution R_meas better or equal on every crystal (16 better, 0
// worse, the rest untouched because their frames never reach the cap), with R_meas 14/4 and ISa 14/6
// in its favour and no measurable cost in wall clock. It is also what jfjoch_viewer already sends.
constexpr int64_t RUGNUX_MAX_SPOT_COUNT = 1000;
// Default rot3d per-frame scale-G smoothing range (XDS DELPHI-like), in degrees of rotation.
constexpr double SMOOTH_G_DEFAULT_DEG = 5.0;
@@ -69,7 +77,7 @@ void print_usage() {
std::cout << " --spot-false-pixels <num> Adaptive detection operating point: expected noise pixels tolerated per frame (default: 100; implies --adaptive-spots)" << std::endl;
std::cout << " --spot-high-resolution <num> High resolution limit for spot finding. If omitted (or 0), spot finding is not clipped in resolution and extends as far as the detector reaches" << std::endl;
std::cout << " --spot-low-resolution <num> Low resolution limit for spot finding, in A (default: 50; lower it, e.g. 24, to exclude the direct-beam halo on weakly-diffracting serial data)" << std::endl;
std::cout << " --max-spots <num> Max spot count (default: 250)" << std::endl;
std::cout << " --max-spots <num> Max spot count per image, the strongest ones, handed to indexing (default: 1000)" << std::endl;
std::cout << " --detect-ice-rings[=on|off] Flag ice-ring spots (de-prioritised in indexing) and exclude ice-ring reflections from scaling/merging; overrides the dataset/master-file setting (default: use dataset value)" << std::endl;
std::cout << std::endl;
@@ -1442,10 +1450,9 @@ static int RunRugnux(int argc, char **argv) {
refine_geometry = 200;
}
if (max_spot_count_override.has_value()) {
experiment.MaxSpotCount(max_spot_count_override.value());
experiment.MaxSpotCount(max_spot_count_override.value_or(RUGNUX_MAX_SPOT_COUNT));
if (max_spot_count_override.has_value())
logger.Info("Max spot count overridden to {}", max_spot_count_override.value());
}
// X-ray bandwidth: CLI overrides the value carried in the dataset; otherwise
// keep whatever the dataset provided (0 / none -> monochromatic).