Jungfraujoch/image_analysis/spot_finding/SpotFindingSettings.h

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#pragma once

#include <cstddef>
#include <optional>
#include <cstdint>
#include <vector>

// Strong pixels above which the connected-component search gives up on a frame, unlabelled: an image
// with this much of the detector over threshold is not a diffraction pattern, and it is what the
// spot extractor's buffers are sized to. It is no longer a time limit - the search is linear in the
// strong pixels either way, and a fully lit 18-megapixel frame labels in 0.16 s.
//
// The bar has to be a FRACTION of the detector. It stood at a fixed 65535, which is one pixel in 64
// of the JUNGFRAU 4M it was written for; left fixed while the detectors grew it became one pixel in
// 276 of an 18-megapixel EIGER - a bar a strongly diffracting crystal clears on its best frames,
// which were then dropped whole, and in silence. One in 64 everywhere, and never below the value
// that used to stand here, so no smaller detector loses ground.
constexpr uint32_t StrongPixelLimit(size_t pixel_count) {
    const auto limit = static_cast<uint32_t>(pixel_count / 64);
    return limit > UINT16_MAX ? limit : UINT16_MAX;
}

// A connected component this size or smaller is judged on size alone. That is where the size bound
// stood before it was raised, so every component that used to be accepted still is.
constexpr int64_t SPOT_SHAPE_FREE_PIXELS = 50;
// A larger one must also be COMPACT: it has to fill at least this percent of the square its bounding
// box fits inside. A Bragg reflection is round and fills about half of that square however bright it
// is; an ice arc, a cosmic-ray track or a lit detector row fills a fifth or less, and those are what
// an upper bound on spot size was ever for.
//
// It is INERT on every dataset it has been measured on: gate on and gate off give a byte-identical
// merge on three rotation crystals including the strongly diffracting one the raised bound was written
// for. The raised bound is what did nearly all of the work there - of the components an absolute ring
// contour pushes past 50 pixels, this shape test rejects a few percent and the raise re-admits the
// rest.
//
// Both only matter while a spot's footprint can grow with its brightness, and since the adaptive
// finder intersects its ring threshold with the local-box SNR test the footprint is peak-relative and
// no component on that set reaches 50 pixels at all.
//
// The shape test is kept anyway because it is the one of the two that does not go stale: a size bound
// is a bet on how large spots are, and the detectors and the detection rule both move underneath it -
// under every peak-relative detector tried, the 200-pixel bound became unreachable while this test
// still fired. The bound is kept alongside it because the cap the local box imposes scales with the
// spot WIDTH, so a set with wider spots than the ones measured here will reach past 50 pixels again.
// A shape test rather than a size test is what XDS and DISTL bound spots with; neither uses this
// statistic, but the choice of shape over size is theirs.
// Following Kabsch (2010) Acta Cryst. D66, 125-132 and Zhang, Sauter et al. (2006) J. Appl. Cryst. 39, 112-119
constexpr int64_t SPOT_MIN_FILL_PERCENT = 20;

// Integer arithmetic throughout, so the host and the GPU extractor agree by construction.
constexpr bool SpotShapeAccepted(int64_t pixel_count, int64_t bbox_side) {
    if (pixel_count <= SPOT_SHAPE_FREE_PIXELS)
        return true;
    return pixel_count * 100 >= SPOT_MIN_FILL_PERCENT * bbox_side * bbox_side;
}

struct SpotFindingSettings {
    bool enable = true;
    float signal_to_noise_threshold = 4.0;  // STRONG_PIXEL in XDS
    int64_t photon_count_threshold = 10;  // Threshold in photon counts
    // Minimum connected pixels per spot. std::nullopt = choose it per image: on the stills indexing
    // path the frame is indexed at min-pix 3/2/1 and the one maximising indexed count x indexed fraction
    // is kept (see MXAnalysisWithoutFPGA::Analyze); a value fixes it. Defaults to a concrete value, so
    // the online receiver and the FPGA path keep the single-pass fixed behaviour unless set otherwise.
    std::optional<int64_t> min_pix_per_spot = 2;
    // Maximum pixels per spot. A component above SPOT_SHAPE_FREE_PIXELS must also pass
    // SpotShapeAccepted, so this bounds how large a ROUND spot may be, not how bright.
    int64_t max_pix_per_spot = 200;
    // High-resolution limit for spot finding [A]. std::nullopt = as far as the detector reaches, i.e. no
    // resolution clipping of the detection at all (DiffractionExperiment::GetDetectorMaxResolution_A
    // supplies the number where one is needed, e.g. for the spot plot's shells).
    std::optional<float> high_resolution_limit;
    // Low-resolution limit for spot finding [A]. std::nullopt = no limit at the low-resolution end, the
    // mirror of high_resolution_limit above. Optional rather than a zero sentinel because zero is not a
    // natural "no limit" here: every pixel has d above it, so the plain comparison would mask the whole
    // image rather than none of it. Defaults to a concrete value, which is where the detection normally
    // stops - the direct beam and its halo sit beyond it.
    std::optional<float> low_resolution_limit = 50.0;
    float cutoff_spot_count_low_res = 5.0;
    std::optional<float> high_res_gap_Q_recipA = 1.5; // 0.25 * 2 * pi

    // Half-width of the ice-ring exclusion band in q (2*pi/d). Measured hexagonal-ice ring FWHM on the
    // JUNGFRAU is ~0.06 q, so the band half-width is ~0.03; 0.02 under-covered the strong low-res rings.
    float ice_ring_width_Q_recipA = 0.03;

    // Powder rings measured from this run's own spots (ring centres in q = 2*pi/d), flagged alongside
    // the fixed hexagonal-ice bands. Hexagonal ice is not the only thing that powders - a shower of
    // microcrystals around the crystal, or salt out of the cryoprotectant, leaves the same textured
    // rings at d-spacings no fixed list can name - and their spots are otherwise handed to the indexer
    // as if they were this crystal's. Empty on a run that shows no such rings, which is nearly all of
    // them; filled by the first pass only where excluding the rings is what lets the run index.
    std::vector<float> measured_ring_q_recipA;

    bool indexing = true;
    bool quick_integration = true;

    // Self-calibrating detection (offline/rugnux path): when true, the fixed photon_count_threshold is
    // replaced by a per-resolution-ring threshold set from the image's own noise (see
    // AdaptiveSpotFinderCPU), so the same setting adapts across datasets with no per-dataset tuning.
    // false_pixels_per_frame is the one portable knob: the expected number of noise pixels tolerated
    // per frame (the threshold's operating point), ~100 for a multi-megapixel detector.
    bool adaptive_threshold = false;
    float false_pixels_per_frame = 100.0f;
    // Detector units per photon of the frames (BraggIntegrationSettings::pixel_gain, set from the same
    // number): the adaptive threshold's Poisson arm and its one-photon floor are taken in photons.
    // 1 for a detector that counts photons.
    float adu_per_photon = 1.0f;
};