Jungfraujoch/image_analysis/scale_merge/RfreeFlags.cpp

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#include "RfreeFlags.h"

#include <algorithm>
#include <unordered_map>
#include <unordered_set>

#include "HKLKey.h"

namespace {
    // splitmix64 bit-mix of a key -> uniform double in [0, 1). Same key -> same value, so all
    // mates of a reflection (which share the Laue-ASU key) get the same draw. Same idiom as the
    // CC1/2 half-set split (HalfForImage in Merge.cpp).
    double UniformFromKey(uint64_t key) {
        uint64_t z = key + 0x9e3779b97f4a7c15ULL;
        z = (z ^ (z >> 30)) * 0xbf58476d1ce4e5b9ULL;
        z = (z ^ (z >> 27)) * 0x94d049bb133111ebULL;
        z = z ^ (z >> 31);
        return static_cast<double>(z >> 11) * (1.0 / 9007199254740992.0);
    }
}

void AssignRfreeFlags(std::vector<MergedReflection> &merged, const gemmi::SpaceGroup &space_group,
                      double rfree_fraction, int min_free_reflections) {
    for (auto &r : merged)
        r.rfree_flag = false;
    if (rfree_fraction <= 0.0 || merged.empty())
        return;

    // The flag is a pure function of the Friedel-merged (Laue) ASU key: symmetry- and Friedel-
    // equivalent reflections collapse to one key and so share a flag (a Bijvoet pair I(+)/I(-) is
    // never split across the work and free sets), and the draw depends only on the reflection index
    // - not on this dataset's resolution range or which reflections it happens to contain. So every
    // dataset of one crystal form gets the SAME free set, which is what a multi-dataset campaign
    // (ensemble refinement, PanDDA) needs. A uniform hash draws ~rfree_fraction of the distinct
    // reflections free; a stratified per-shell draw would be tied to the dataset and break that.
    const HKLKeyGenerator laue_key(/*merge_friedel=*/true, space_group);

    // Count the distinct test-eligible reflections (distinct Laue-ASU keys; mates collapse to one) so
    // the fraction can be floored to a usable test-set size on small data.
    std::unordered_set<uint64_t> distinct;
    distinct.reserve(merged.size());
    for (const auto &r : merged)
        distinct.insert(laue_key(r).pack());

    // Effective fraction: at least rfree_fraction, lifted toward min_free_reflections/N on small data
    // (so R-free is not sampling-noise dominated), but the floor's lift is capped at MAX_FRACTION so a
    // large test set never steals working data. An explicitly large rfree_fraction is always honoured.
    constexpr double MAX_FRACTION = 0.10;
    const double floor_fraction =
        std::min(min_free_reflections / static_cast<double>(distinct.size()), MAX_FRACTION);
    const double eff_fraction = std::max(rfree_fraction, floor_fraction);

    for (auto &r : merged)
        r.rfree_flag = UniformFromKey(laue_key(r).pack()) < eff_fraction;
}

size_t ApplyReferenceFreeFlags(std::vector<MergedReflection> &merged, const gemmi::SpaceGroup &space_group,
                               const std::vector<MergedReflection> &reference) {
    // Reference free/work partition keyed by the Friedel-merged (Laue) ASU index, so it transfers
    // regardless of which Bijvoet mate / symmetry equivalent each dataset happens to have measured.
    const HKLKeyGenerator laue_key(/*merge_friedel=*/true, space_group);
    std::unordered_map<uint64_t, bool> ref_flag;
    ref_flag.reserve(reference.size());
    for (const auto &r : reference)
        ref_flag[laue_key(r).pack()] = r.rfree_flag;

    size_t matched = 0;
    for (auto &r : merged) {
        const auto it = ref_flag.find(laue_key(r).pack());
        if (it != ref_flag.end()) {          // reflections absent from the reference keep their hash flag
            r.rfree_flag = it->second;
            ++matched;
        }
    }
    return matched;
}