leonarski_fandClaude Opus 5
16bf3408f0
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>
42 lines
2.2 KiB
C++
42 lines
2.2 KiB
C++
// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <optional>
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#include <cstdint>
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struct SpotFindingSettings {
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bool enable = true;
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float signal_to_noise_threshold = 4.0; // STRONG_PIXEL in XDS
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int64_t photon_count_threshold = 10; // Threshold in photon counts
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// Minimum connected pixels per spot. std::nullopt = choose it per image: on the stills indexing
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// path the frame is indexed at min-pix 3/2/1 and the one maximising indexed count x indexed fraction
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// is kept (see MXAnalysisWithoutFPGA::Analyze); a value fixes it. Defaults to a concrete value, so
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// the online receiver and the FPGA path keep the single-pass fixed behaviour unless set otherwise.
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std::optional<int64_t> min_pix_per_spot = 2;
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int64_t max_pix_per_spot = 50; // Maximum pixels per spot
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// High-resolution limit for spot finding [A]. std::nullopt = as far as the detector reaches, i.e. no
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// resolution clipping of the detection at all (DiffractionExperiment::GetDetectorMaxResolution_A
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// supplies the number where one is needed, e.g. for the spot plot's shells).
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std::optional<float> high_resolution_limit;
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float low_resolution_limit = 50.0;
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float cutoff_spot_count_low_res = 5.0;
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std::optional<float> high_res_gap_Q_recipA = 1.5; // 0.25 * 2 * pi
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// Half-width of the ice-ring exclusion band in q (2*pi/d). Measured hexagonal-ice ring FWHM on the
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// JUNGFRAU is ~0.06 q, so the band half-width is ~0.03; 0.02 under-covered the strong low-res rings.
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float ice_ring_width_Q_recipA = 0.03;
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bool indexing = true;
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bool quick_integration = true;
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// Self-calibrating detection (offline/rugnux path): when true, the fixed photon_count_threshold is
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// replaced by a per-resolution-ring threshold set from the image's own noise (see
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// AdaptiveSpotFinderCPU), so the same setting adapts across datasets with no per-dataset tuning.
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// false_pixels_per_frame is the one portable knob: the expected number of noise pixels tolerated
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// per frame (the threshold's operating point), ~100 for a multi-megapixel detector.
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bool adaptive_threshold = false;
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float false_pixels_per_frame = 100.0f;
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};
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