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Jungfraujoch/image_analysis/IndexAndRefine.h
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leonarski_fandClaude Opus 5 16bf3408f0 Address code-review findings; make detection limits detector-driven 
One changeset, developed together in response to a review of this branch, so the
files carry several of the changes at once. Full test suite passes (733 cases).

Spot finding
- Split ImageSpotFinder into Detect() (flag strong pixels - the expensive
  per-pixel pass) and ExtractSpots() (CCL + min/max-pix + resolution mask), with
  Run() = both. The per-image min-pix escalation now detects ONCE and repeats
  only the cheap extraction, instead of re-running the whole finder four times
  per frame as it did on the default path. It also keeps the winning attempt's
  spot list rather than re-extracting it, so the frame that is integrated is
  exactly the frame that was scored - which a GPU re-extract could not guarantee
  (float atomic ordering).
- spot_finding_time_s no longer swallows indexing time, and indexing_time_s now
  sums every escalation call instead of reporting only the last.

Detection limits follow the detector
- The azimuthal-integration upper q and the spot-finding high-resolution limit
  are now std::optional, in the C++ structs AND in the OpenAPI schema, and
  resolve to the detector's own maximum (DiffractionExperiment::GetDetectorMaxQ_
  recipA). Adaptive detection reads a pixel's ring from the azimuthal bins, so a
  pixel outside that q range could never be strong - the integration range
  silently bounded what detection could see, regardless of the requested
  resolution limit. Regenerated the C++ and TypeScript clients; the viewer and
  the web frontend each gained a "to detector edge" switch.

Detection defaults are now per workflow (measured, not assumed)
- Stills: adaptive detection, min-pix chosen per image, no resolution clipping.
- Rotation: fixed-threshold finder, min-pix 2, 1.5 A limit.
  On a 33-crystal rotation battery, adaptive detection helped four hard crystals
  but deterministically broke three (a lost space group, a halved indexing rate,
  a collapsed merge), and the detector-edge limit cost indexing on a strong
  rotation set (100.0 -> 96.8%). Each is still overridable by its flag, and
  --no-adaptive-spots is new.

Indexer seed escalation
- Stop escalating once a seed's lattice explains >= 90% of the seed spots.
  Previously any frame with >= 80 spots always paid three indexer calls, online
  broker included.

Merge-consistency filter
- --min-image-cc gated on a per-image CC computed BEFORE the stills partiality
  post-refinement and never refreshed; the refiner now recomputes it, so the
  reported CC describes the data that are actually merged.
- Replaced the per-call cc_mask argument with one MergeOnTheFly flag, so the
  merge, the error model and MergeStats can no longer disagree about which
  images are in (the --scale path merged unfiltered while its statistics were
  filtered).

Per-image B-factor refinement (-B) removed
- Measured on four serial-stills datasets: it is a no-op where the per-image fit
  is well conditioned and actively harmful where it is not (CC1/2 -8.1, R_meas
  +23.2 on the weakest large-cell set, whose fits hit their [-50, 200] bounds on
  14-25% of images). It had also been silently DISCARDED since the partiality
  post-refinement landed - reported but not applied. Rather than fix and keep a
  knob with no demonstrated benefit, the flag and the whole image_scale_b_factor
  chain are gone: setting, scaling fit, message field, CBOR, HDF5 write and
  read-back, per-image plot, OpenAPI enum, viewer column and checkbox, docs.
  ScaleOnTheFly no longer needs Ceres at all - the fit is a linear IRLS.
  (The Wilson per-image b_factor is a different quantity and stays.)

Stills partiality width now fits both of its components
- sigma^2 = gamma0^2 + (gamma_e*d*)^2 instead of a purely angular gamma_e*d*
  with gamma0 pinned to 0. Fitted per crystal by least squares of dist_ewald^2
  on d*^2. The angular-only width is fitted over a d*^2-dense population, so it
  was pinned by the high-resolution edge and collapsed at low d*: median
  partiality 0.008 beyond 13 A for reflections that were plainly recorded, 55%
  of them under the merge's partiality floor, and the survivors divided by those
  values - which inflated the merged low-resolution intensity scale 3.6x
  (~ +9 A^2 of apparent B). Measured on 5000 stills: the ramp flattens to 0.89x,
  no observation is dropped any more (701750 -> 716811), shell-mean CC1/2 and
  R-free improve slightly. Note CC1/2, R_meas, completeness and a B-refining
  R-free are all blind to that ramp, which is why it survived earlier validation;
  the cost is high-resolution R_meas (98.5 -> 101.9 shell-averaged).

Removed dead code from add-then-remove churn
- Prediction-time "still partiality" (unreachable: no setter), the phantom
  IndexingSettings::min_indexed_spot_fraction knob (getter, no setter - now the
  constant it always was), StillsPartialityRefine's caller-less Settings
  constructor and its reference to a long-gone env var, ProcessImage's unread
  bool return, an unused include, and a dead viewer overlay hook.

Also
- Viewer: the magnifier compared a QImage with itself, so its scene rect was set
  once ever and it could not pan into a larger dataset; the hover tail timer
  could fire after leaveEvent and resurrect the resolution readout outside the
  image.
- update_version.sh regenerated the frontend lock file BEFORE bumping the
  version (every release shipped an off-by-one lock), and did git rm/git add on
  a path that has not existed since the client moved to src/client - with no
  set -e, both failed silently.
- fpga/pcie_driver/postinstall.sh tested "[ ! occurrences > 0 ]", which is a
  redirect, not a test, so dkms add never ran.
- Unit tests for the adaptive-threshold host functions, which had none.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-07-27 09:07:00 +02:00

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// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
#include <vector>
#include <mutex>
#include <functional>
#include "../common/DiffractionSpot.h"
#include "../common/DiffractionExperiment.h"
#include "../common/AzimuthalIntegrationMapping.h"
#include "../common/AzimuthalIntegrationProfile.h"
#include "../common/Reflection.h"
#include "bragg_prediction/BraggPrediction.h"
#include "indexing/IndexerThreadPool.h"
#include "lattice_search/LatticeSearch.h"
#include "rotation_indexer/RotationIndexer.h"
#include "rotation_indexer/RotationIndexerCounter.h"
#include "scale_merge/ReindexAmbiguity.h"
#include "scale_merge/ScaleOnTheFly.h"
#include "scale_merge/ScalingResult.h"
#include "IntegrationOutcome.h"
// Integrates the predicted reflections off whatever image the caller holds: the preprocessed GPU/CPU
// buffer on the WithoutFPGA path (GPU when available), or the assembled detector image read straight,
// on the CPU, on the forced-CPU FPGA path. Keeps IndexAndRefine independent of the image representation.
using BraggIntegrateFn = std::function<std::vector<Reflection>(
const std::vector<Reflection> &predicted, size_t npredicted, int64_t image_number)>;
class IndexAndRefine {
const bool index_ice_rings;
// When false, the current image's result is still returned via the outgoing message, but the
// whole-run integration_outcome vector is not retained (viewer live/interactive use, which never
// scales the accumulated run). rugnux/receiver keep it true so ScaleAllImages/merge have the data.
const bool retain_outcomes_;
const DiffractionExperiment& experiment;
const DiffractionGeometry geom_;
std::optional<CrystalLattice> indexed_lattice;
std::optional<GoniometerAxis> axis_;
IndexerThreadPool *indexer_;
std::unique_ptr<RotationIndexer> rotation_indexer;
RotationIndexerCounter rotation_indexer_counter;
struct IndexingOutcome {
std::optional<CrystalLattice> lattice_candidate;
std::vector<CrystalLattice> extra_lattice_candidates;
std::vector<Coord> extra_lattice_rotations;
DiffractionExperiment experiment;
LatticeMessage symmetry{
.centering = 'P',
.niggli_class = 0,
.crystal_system = gemmi::CrystalSystem::Triclinic
};
bool beam_center_updated = false;
explicit IndexingOutcome(const DiffractionExperiment& experiment_ref)
: experiment(experiment_ref) {}
};
mutable std::mutex reflections_mutex;
std::vector<IntegrationOutcome> integration_outcome;
std::vector<float> mosaicity;
// Optional per-frame mosaicity used for Bragg prediction, indexed by image number. When set (the
// second pass of the rotation two-pass), it overrides the per-image spot-shape estimate so prediction
// uses the frame-order-SMOOTHED mosaicity that RotationScaleMerge already fitted in the first pass,
// rather than re-deriving it from scratch.
std::vector<float> prediction_mosaicity_override_;
std::vector<float> scale_cc;
std::vector<std::optional<UnitCell> > unit_cells;
IndexingOutcome DetermineLatticeAndSymmetryRotation(DataMessage &msg);
IndexingOutcome DetermineLatticeAndSymmetry(DataMessage &msg);
// Shared indexing path: determine the lattice/symmetry, refine geometry, and run AnalyzeIndexing.
// Returns the outcome (ready for integration) when the frame indexes, nullopt otherwise. Both the
// real per-image ProcessImage and the first-pass scheme validation go through this, so they cannot
// diverge.
std::optional<IndexingOutcome> DetermineRefineAnalyze(DataMessage &msg,
const SpotFindingSettings &spot_finding_settings);
void RefineGeometryIfNeeded(DataMessage &msg, IndexingOutcome &outcome);
void QuickPredictAndIntegrate(DataMessage &msg,
const SpotFindingSettings &spot_finding_settings,
BraggPrediction &prediction,
const BraggIntegrateFn &integrate,
const IndexingOutcome &outcome);
std::unique_ptr<ReindexAmbiguityResolver> reindex_resolver;
void ScaleImage(DataMessage &msg, IntegrationOutcome& outcome);
std::optional<float> RotationAngle(int64_t image) const; // mid-exposure angle for the indexer
public:
IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool *indexer, bool retain_outcomes = true);
void AddImageToRotationIndexer(DataMessage &msg);
void ForceRotationIndexerLattice(const CrystalLattice& lattice);
void ForceRotationIndexerResult(const RotationIndexerResult& result);
// Supply a per-frame (by image number) mosaicity for prediction, overriding the per-image estimate.
void SetPredictionMosaicityOverride(std::vector<float> mosaicity_per_frame) {
prediction_mosaicity_override_ = std::move(mosaicity_per_frame);
}
// Returns whether the frame indexed (a lattice was found and refined). Integration, when it runs,
// is a further step gated on quick_integration.
void ProcessImage(DataMessage &msg, const SpotFindingSettings &settings,
BraggPrediction &prediction, const BraggIntegrateFn &integrate);
// Index a single frame (no integration) with the current forced rotation lattice; used to score
// first-pass sampling schemes on the real per-image path. Returns whether the frame indexed.
bool IndexFrameOnly(DataMessage &msg, const SpotFindingSettings &settings);
IndexAndRefine& ReferenceIntensities(std::vector<MergedReflection> &reference);
ScalingResult ScaleAllImages(const std::vector<MergedReflection> &reference, size_t nthreads = 0);
std::optional<RotationIndexerResult> FinalizeRotationIndexing();
std::optional<UnitCell> GetConsensusUnitCell() const;
// Not thread safe, need to be run after processing is all done
const std::vector<float> &GetImageCC() const;
const std::vector<std::optional<UnitCell> > &GetUnitCells() const;
std::vector<IntegrationOutcome> &GetIntegrationOutcome();
const std::vector<IntegrationOutcome> &GetIntegrationOutcome() const;
};
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