Jungfraujoch/image_analysis/beam_stop/ShadowFinder.cpp

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

#include "ShadowFinder.h"

#include <algorithm>
#include <cmath>
#include <limits>
#include <queue>
#include <type_traits>

#include "../../common/JFJochException.h"

// A pixel is shadow when its background is below this fraction of the background it is
// compared against.
constexpr float SHADOW_RATIO = 0.35f;

// The boundary grows outward into partially shadowed pixels down to this fraction, but no
// further than PENUMBRA_MAX_PX from the core.
constexpr float PENUMBRA_RATIO = 0.72f;
constexpr int   PENUMBRA_MAX_PX = 14;

// Bridge module gaps and small breaks that the holder arm crosses.
constexpr int BRIDGE_PX = 6;

// A pixel whose maximum reaches this recorded a real reflection and is never masked - a
// beam stop cannot block a reflection that was measured.
constexpr int64_t MIN_REFLECTION = 25;

// Counts the background must have accumulated over the frames and the pooled pixels before
// a dip in it is believable. Below this a Poisson hole is indistinguishable from a shadow,
// and testing anyway masks whole detectors on low-background data.
constexpr double MIN_EXPECTED_COUNTS = 60;

// Side of the box the background is pooled over before testing, and how far out the radial
// comparison looks for unshadowed background.
constexpr int   POOL_PX = 5;
constexpr float ENVELOPE_MM = 6.0f;

// Binary-image helpers on a width*height frame stored row-major as char (0/1). All run once,
// at GetMask() time; the BFS forms keep them O(pixels) rather than O(pixels * radius).
namespace {

// 8-connected dilation by `r` pixels (Chebyshev), via a multi-source BFS.
std::vector<char> dilate(const std::vector<char> &in, int W, int H, int r) {
    if (r <= 0)
        return in;
    std::vector<int> dist(in.size(), -1);
    std::queue<int> q;
    for (size_t i = 0; i < in.size(); i++)
        if (in[i]) { dist[i] = 0; q.push(static_cast<int>(i)); }
    while (!q.empty()) {
        const int i = q.front(); q.pop();
        if (dist[i] >= r)
            continue;
        const int y = i / W, x = i % W;
        for (int dy = -1; dy <= 1; dy++)
            for (int dx = -1; dx <= 1; dx++) {
                const int yy = y + dy, xx = x + dx;
                if (yy < 0 || yy >= H || xx < 0 || xx >= W)
                    continue;
                const int j = yy * W + xx;
                if (dist[j] < 0) { dist[j] = dist[i] + 1; q.push(j); }
            }
    }
    std::vector<char> out(in.size());
    for (size_t i = 0; i < out.size(); i++)
        out[i] = (dist[i] >= 0) ? 1 : 0;
    return out;
}

// Erosion by `r` = dilation of the complement; outside the frame counts as complement.
std::vector<char> erode(const std::vector<char> &in, int W, int H, int r) {
    std::vector<char> comp(in.size());
    for (size_t i = 0; i < in.size(); i++)
        comp[i] = !in[i];
    const auto grown = dilate(comp, W, H, r);
    std::vector<char> out(in.size());
    for (size_t i = 0; i < out.size(); i++)
        out[i] = !grown[i];
    return out;
}

// Pixels of `passable` reachable from any of `seeds` (8-connected flood).
std::vector<char> flood(const std::vector<char> &passable, int W, int H, const std::vector<int> &seeds) {
    std::vector<char> visited(passable.size(), 0);
    std::queue<int> q;
    for (const int s : seeds)
        if (passable[s] && !visited[s]) { visited[s] = 1; q.push(s); }
    while (!q.empty()) {
        const int i = q.front(); q.pop();
        const int y = i / W, x = i % W;
        for (int dy = -1; dy <= 1; dy++)
            for (int dx = -1; dx <= 1; dx++) {
                const int yy = y + dy, xx = x + dx;
                if (yy < 0 || yy >= H || xx < 0 || xx >= W)
                    continue;
                const int j = yy * W + xx;
                if (passable[j] && !visited[j]) { visited[j] = 1; q.push(j); }
            }
    }
    return visited;
}

// Fill holes: background not reachable from the image border becomes region.
std::vector<char> fill_holes(const std::vector<char> &region, int W, int H) {
    std::vector<char> bg_visited(region.size(), 0);
    std::queue<int> q;
    auto push = [&](int i) { if (!region[i] && !bg_visited[i]) { bg_visited[i] = 1; q.push(i); } };
    for (int x = 0; x < W; x++) { push(x); push((H - 1) * W + x); }
    for (int y = 0; y < H; y++) { push(y * W); push(y * W + W - 1); }
    while (!q.empty()) {
        const int i = q.front(); q.pop();
        const int y = i / W, x = i % W;
        for (int dy = -1; dy <= 1; dy++)
            for (int dx = -1; dx <= 1; dx++) {
                const int yy = y + dy, xx = x + dx;
                if (yy < 0 || yy >= H || xx < 0 || xx >= W)
                    continue;
                const int j = yy * W + xx;
                if (!region[j] && !bg_visited[j]) { bg_visited[j] = 1; q.push(j); }
            }
    }
    std::vector<char> out = region;
    for (size_t i = 0; i < out.size(); i++)
        if (!region[i] && !bg_visited[i])
            out[i] = 1;
    return out;
}

// Sum of `in` over the k x k box centred on each pixel, zero outside the frame.
std::vector<double> box_sum(const std::vector<double> &in, int W, int H, int k) {
    const int half = k / 2;
    std::vector<double> row(in.size(), 0.0), out(in.size(), 0.0);
    for (int y = 0; y < H; y++) {
        double s = 0;
        for (int x = 0; x <= std::min(half, W - 1); x++)
            s += in[y * W + x];
        for (int x = 0; x < W; x++) {
            row[y * W + x] = s;
            if (x + half + 1 < W) s += in[y * W + x + half + 1];
            if (x - half >= 0)    s -= in[y * W + x - half];
        }
    }
    for (int x = 0; x < W; x++) {
        double s = 0;
        for (int y = 0; y <= std::min(half, H - 1); y++)
            s += row[y * W + x];
        for (int y = 0; y < H; y++) {
            out[y * W + x] = s;
            if (y + half + 1 < H) s += row[(y + half + 1) * W + x];
            if (y - half >= 0)    s -= row[(y - half) * W + x];
        }
    }
    return out;
}

// Median of `values` per integer radius, over the pixels flagged in `use`.
std::vector<float> ring_median(const std::vector<float> &values, const std::vector<char> &use,
                               const std::vector<int> &radius, int max_radius) {
    std::vector<std::vector<float>> bins(max_radius + 1);
    for (size_t i = 0; i < values.size(); i++)
        if (use[i])
            bins[radius[i]].push_back(values[i]);
    std::vector<float> median(max_radius + 1, 0.0f);
    for (int r = 0; r <= max_radius; r++) {
        auto &b = bins[r];
        if (!b.empty()) {
            const size_t k = b.size() / 2;
            std::nth_element(b.begin(), b.begin() + k, b.end());
            median[r] = b[k];
        }
    }
    return median;
}

// Largest baseline over [r, r + win] - the background just outside radius r.
std::vector<float> outer_envelope(const std::vector<float> &baseline, int win) {
    const int n = static_cast<int>(baseline.size());
    std::vector<float> out(n, 0.0f);
    for (int r = 0; r < n; r++) {
        float v = baseline[r];
        for (int k = 1; k <= win; k++)
            v = std::max(v, baseline[std::min(r + k, n - 1)]);
        out[r] = v;
    }
    return out;
}

}  // namespace

ShadowFinder::ShadowFinder(const DiffractionExperiment &experiment, const PixelMask &mask)
    : width(static_cast<int>(experiment.GetXPixelsNumConv())),
      height(static_cast<int>(experiment.GetYPixelsNumConv())),
      beam_x(experiment.GetBeamX_pxl()),
      beam_y(experiment.GetBeamY_pxl()),
      envelope_px(std::max(4, static_cast<int>(std::lround(ENVELOPE_MM / experiment.GetPixelSize_mm())))),
      pixel_mask(mask.GetMask(experiment)),
      max_value(static_cast<size_t>(width) * height, 0),
      sum_value(static_cast<size_t>(width) * height, 0),
      valid_count(static_cast<size_t>(width) * height, 0) {
    if (pixel_mask.size() != max_value.size())
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "ShadowFinder: pixel mask does not match the detector");
}

template<class T>
void ShadowFinder::Add(const T *ptr) {
    // The pixel type's sentinel extreme marks "no data" (module gap / masked): the
    // preprocessor/writer stores INT*_MIN for signed and UINT*_MAX for unsigned. For signed
    // types the opposite extreme is a genuine saturated value and is kept, so a saturated
    // reflection still registers as bright.
    T masked;
    if constexpr (std::is_signed_v<T>)
        masked = std::numeric_limits<T>::min();
    else
        masked = std::numeric_limits<T>::max();

    std::unique_lock ul(m);
    for (size_t i = 0; i < max_value.size(); i++) {
        const T v = ptr[i];
        if (v == masked)
            continue;
        const int64_t vi = static_cast<int64_t>(v);
        if (valid_count[i] == 0 || vi > max_value[i])
            max_value[i] = vi;
        sum_value[i] += vi;
        valid_count[i]++;
    }
    frames++;
}

void ShadowFinder::AddImage(const DataMessage &data, std::vector<uint8_t> buffer) {
    if (static_cast<size_t>(data.image.GetWidth()) * data.image.GetHeight() != max_value.size())
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "ShadowFinder: image size does not match the detector");

    const auto ptr = data.image.GetUncompressedPtr(buffer);
    switch (data.image.GetMode()) {
        case CompressedImageMode::Int8:   Add(reinterpret_cast<const int8_t   *>(ptr)); break;
        case CompressedImageMode::Uint8:  Add(reinterpret_cast<const uint8_t  *>(ptr)); break;
        case CompressedImageMode::Int16:  Add(reinterpret_cast<const int16_t  *>(ptr)); break;
        case CompressedImageMode::Uint16: Add(reinterpret_cast<const uint16_t *>(ptr)); break;
        case CompressedImageMode::Int32:  Add(reinterpret_cast<const int32_t  *>(ptr)); break;
        case CompressedImageMode::Uint32: Add(reinterpret_cast<const uint32_t *>(ptr)); break;
        default:
            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                  "ShadowFinder: unsupported image mode");
    }
}

uint32_t ShadowFinder::GetFrameCount() const {
    std::unique_lock ul(m);
    return frames;
}

std::vector<uint32_t> ShadowFinder::GetMask() const {
    std::unique_lock ul(m);

    const int W = width, H = height;
    const int n_pixels = W * H;

    std::vector<uint32_t> mask(n_pixels, 0);
    if (frames == 0)
        return mask;

    // mean projection, usable pixels and radius from the beam centre
    std::vector<float> mean(n_pixels, 0.0f);
    std::vector<char>  valid(n_pixels, 0);
    std::vector<int>   radius(n_pixels, 0);
    int max_radius = 0;
    for (int y = 0; y < H; y++)
        for (int x = 0; x < W; x++) {
            const int i = y * W + x;
            if (valid_count[i] > 0 && pixel_mask[i] == 0) {
                mean[i] = static_cast<float>(static_cast<double>(sum_value[i]) / valid_count[i]);
                valid[i] = 1;
            }
            const float dx = x - beam_x, dy = y - beam_y;
            radius[i] = static_cast<int>(std::lround(std::sqrt(dx * dx + dy * dy)));
            max_radius = std::max(max_radius, radius[i]);
        }

    // Pool the background over a small box before testing it. A background of a fraction of
    // a count per pixel per frame gives no single pixel enough counts to tell a shadow from
    // a Poisson hole; the stop and its arm are wider than the box, so pooling costs no
    // resolution that matters and multiplies the statistics by the pixels in the box.
    std::vector<double> num(n_pixels), den(n_pixels);
    for (int i = 0; i < n_pixels; i++) {
        num[i] = valid[i] ? mean[i] : 0.0;
        den[i] = valid[i] ? 1.0 : 0.0;
    }
    const auto pooled_sum = box_sum(num, W, H, POOL_PX);
    const auto pooled_count = box_sum(den, W, H, POOL_PX);
    std::vector<float> pooled(n_pixels, 0.0f);
    for (int i = 0; i < n_pixels; i++)
        if (pooled_count[i] > 0)
            pooled[i] = static_cast<float>(pooled_sum[i] / pooled_count[i]);

    // Azimuthal comparison: the median of the ring, iterated so the shadow stays out of the
    // baseline it is measured against.
    std::vector<float> ratio(n_pixels, 1.0f);
    std::vector<char>  excluded(n_pixels, 0);
    std::vector<float> baseline;
    for (int iter = 0; iter < 3; iter++) {
        std::vector<char> use(n_pixels);
        for (int i = 0; i < n_pixels; i++)
            use[i] = valid[i] && !excluded[i];
        baseline = ring_median(pooled, use, radius, max_radius);
        for (int i = 0; i < n_pixels; i++)
            if (valid[i])
                ratio[i] = pooled[i] / std::max(baseline[radius[i]], 1e-6f);
        for (int i = 0; i < n_pixels; i++)
            excluded[i] = valid[i] && ratio[i] < SHADOW_RATIO;
    }

    // Radial comparison: the background just outside this radius. The disk blocks its rings
    // completely, so their median is the shadow itself and only this comparison sees it.
    const auto envelope = outer_envelope(baseline, envelope_px);
    std::vector<float> ratio_radial(n_pixels, 1.0f);
    for (int i = 0; i < n_pixels; i++)
        if (valid[i])
            ratio_radial[i] = pooled[i] / std::max(envelope[radius[i]], 1e-6f);

    // A dip counts only where the background it is compared against was actually counted.
    std::vector<char> low(n_pixels, 0);
    for (int i = 0; i < n_pixels; i++) {
        if (!valid[i])
            continue;
        const double counted = frames * pooled_count[i];
        low[i] = (ratio[i] < SHADOW_RATIO && baseline[radius[i]] * counted >= MIN_EXPECTED_COUNTS)
              || (ratio_radial[i] < SHADOW_RATIO && envelope[radius[i]] * counted >= MIN_EXPECTED_COUNTS);
    }

    // The shadow is the low region connected to the beam centre, bridging the gaps it crosses.
    const std::vector<char> bridged = dilate(low, W, H, BRIDGE_PX);
    std::vector<int> seeds;
    for (int i = 0; i < n_pixels; i++)
        if (radius[i] < 4)
            seeds.push_back(i);
    const std::vector<char> connected = flood(bridged, W, H, seeds);
    std::vector<char> region(n_pixels);
    for (int i = 0; i < n_pixels; i++)
        region[i] = low[i] && connected[i];

    // Recorded reflections. A small cluster is required so a single-frame zinger does not count.
    std::vector<char> lit(n_pixels, 0);
    for (int i = 0; i < n_pixels; i++)
        lit[i] = (valid_count[i] > 0) && (max_value[i] >= MIN_REFLECTION);
    std::vector<char> reflection(n_pixels, 0);
    for (int y = 0; y < H; y++)
        for (int x = 0; x < W; x++) {
            const int i = y * W + x;
            if (!lit[i]) continue;
            int neighbours = 0;
            for (int dy = -1; dy <= 1; dy++)
                for (int dx = -1; dx <= 1; dx++) {
                    const int yy = y + dy, xx = x + dx;
                    if ((dx || dy) && yy >= 0 && yy < H && xx >= 0 && xx < W && lit[yy * W + xx])
                        neighbours++;
                }
            reflection[i] = (neighbours >= 2);
        }

    // Grow the soft boundary, round it and fill the disk interior.
    const std::vector<char> penumbra = dilate(region, W, H, PENUMBRA_MAX_PX);
    for (int i = 0; i < n_pixels; i++)
        if (penumbra[i] && valid[i] && std::min(ratio[i], ratio_radial[i]) < PENUMBRA_RATIO)
            region[i] = 1;

    region = erode(dilate(region, W, H, 2), W, H, 2);
    region = fill_holes(region, W, H);

    // Expose recorded reflections - done last, with no fill afterwards, so a spot the shadow
    // still covered is given back rather than re-enclosed.
    const std::vector<char> reflection_grown = dilate(reflection, W, H, 1);
    for (int i = 0; i < n_pixels; i++)
        if (reflection_grown[i])
            region[i] = 0;

    for (int i = 0; i < n_pixels; i++)
        mask[i] = region[i] ? 1 : 0;
    return mask;
}