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>
60 lines
3.3 KiB
C++
60 lines
3.3 KiB
C++
// SPDX-FileCopyrightText: 2025 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 <vector>
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#include "../../common/DiffractionExperiment.h"
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#include "../IntegrationOutcome.h"
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#include "HKLKey.h"
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// Physical partiality post-refinement for STILLS (on by default; rugnux --simple-stills opts out).
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//
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// The default stills partiality is a frozen scalar-sigma Gaussian (or p == 1): p is set once at
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// prediction and never optimised, and any attempt to free a per-image sigma jointly with the per-image
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// scale G collapses (within one still the excitation-error spread is narrow, so a scalar sigma is
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// degenerate with G). This class instead parametrises partiality by the crystal ORIENTATION - a small
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// tilt (dpsi_x, dpsi_y) about the two axes perpendicular to the beam - shared by all of a crystal's
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// reflections. A tilt moves each reflection's excitation error by an amount that depends on where the
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// reflection sits on the pattern (one side of the Ewald sphere approaches, the opposite recedes), so it
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// reshapes the SPATIAL pattern of partialities in a way a single G cannot mimic. That breaks the
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// degeneracy that killed the scalar-sigma fit.
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//
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// Because the integrated intensity I_obs is fixed, refining the tilt only recomputes the partiality
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// analytically from the stored per-image lattice/geometry (q = A*.h + B*.k + C*.l, then
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// dist_ewald = | |q + S0| - 1/lambda |) - NO pixel re-integration. The loop is: merge -> per-crystal
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// refine tilt (G profiled out by the same robust IRLS ScaleOnTheFly uses) -> recompute p and
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// image_scale_corr -> re-merge, iterated a few times. Mutates each reflection's `partiality` and
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// `image_scale_corr` in place; the existing MergeOnTheFly then consumes the improved corrections.
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class StillsPartialityRefine {
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public:
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struct Settings {
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int outer_iterations = 2; // merge <-> refine cycles
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int inner_iterations = 3; // (solve G) <-> (refine tilt) alternations per crystal
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size_t min_reflections = 40; // skip tilt refinement below this (anti-overfit on sparse crystals)
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double max_tilt_rad = 0.0175; // hard bound on |dpsi| (~1 deg); indexing already refined orientation
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double prior_sigma_deg = 0.02; // soft prior pulling dpsi toward 0 (0 = off); tames weak-data overfit,
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// inert on strong data (well-supported tilts overcome it)
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double robust_k = 3.0; // Cauchy loss scale (sigma units)
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double gamma_e = 0.0; // angular width sigma(d*) = gamma_e*d* (0 = estimate per crystal from data)
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};
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explicit StillsPartialityRefine(const DiffractionExperiment &x);
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// Refine all crystals in place. Returns the mean |dpsi| applied (degrees), for diagnostics.
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double Run(std::vector<IntegrationOutcome> &outcomes, size_t nthreads = 0) const;
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private:
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const DiffractionExperiment experiment_;
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const Settings settings_{};
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const HKLKeyGenerator hkl_key_generator_;
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const std::optional<double> d_min_limit_;
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const double min_partiality_;
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const float bandwidth_sigma_;
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// Refine one crystal against the reference map; returns |dpsi| in degrees (0 if skipped).
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double RefineOne(IntegrationOutcome &outcome,
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const std::map<HKLKey, double> &reference) const;
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};
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