Jungfraujoch/image_analysis/spot_finding/ImageSpotFinderGPU.cu

// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

// GPU Spot finding developed by Hans-Christian Stadler (PSI)
// Copyright (2019-2023) Paul Scherrer Institute

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

struct spot_parameters {
    int32_t width;
    int32_t height;
    float strong_pixel_threshold2;
    int32_t count_threshold;
};

// input      X x Y pixels array
// output     X x Y bit array

static constexpr int WARP_SIZE = 32;    // assume warp size of 32 cuda threads per warp

inline void cuda_err(cudaError_t val) {
    if (val != cudaSuccess)
        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
}

// Write pixel results to bit array
// params: spot finding parameters
// out: pixel result bit array
// pixel: flat pixel index = bit index into bit array
// val: pixel result
// **NOTE**: assumes sizeof(*out) * 8 == WARP_SIZE
__device__ __forceinline__ void write_result(const spot_parameters& params, uint32_t* out, int32_t pixel, uint8_t val)
{
    static_assert(sizeof(*out) * 8 == WARP_SIZE, "Violation of essential implementation assumption: WARP_SIZE must match output array element type bit size!");
    static constexpr unsigned ALL_THREADS = UINT32_MAX;
    const int32_t laneid = threadIdx.x & (WARP_SIZE - 1);
    unsigned result = __ballot_sync(ALL_THREADS, val);
    const int32_t idx = pixel / WARP_SIZE;      // global uint32_t index
    const int32_t bit = pixel % WARP_SIZE;      // local bit index

    if ((bit >= laneid) && (laneid == 0)) {      // write to upper part of uint32_t
        result <<= bit;
        if (result)
            atomicOr(&out[idx], result);
    } else if ((bit < laneid) && (bit == 0)) {   // write to lower part of uint32_t
        result >>= laneid;
        if (result)
            atomicOr(&out[idx], result);
    }
}

// Determine if pixel could be a spot
// params: spot finding parameters
// val: pixel value
// sum: window sum
// sum2: window sum of squares
// count: window valid pixels count
// return the pixel result: 0-no spot / 1-spot candidate
__device__ __forceinline__ uint8_t pixel_result(const spot_parameters& params, const int64_t val, int64_t sum, int64_t sum2, int64_t count)
{
    sum -= val;
    sum2 -= val * val;
    count -= 1;

    const int64_t var = count * sum2 - (sum * sum);   // This should be divided by ((2*NBX+1) * (2*NBY+1)-1)*((2*NBX+1) * (2*NBY+1))
    const int64_t in_minus_mean = val * count - sum;  // Should be divided by ((2*NBX+1) * (2*NBY+1));

    const int64_t tmp1 = in_minus_mean * in_minus_mean;
    const float tmp2 = var * params.strong_pixel_threshold2;
    bool snr_criterion;

    if (params.strong_pixel_threshold2 == 0.0f)
        snr_criterion = true;
    else
        snr_criterion = (count > ImageSpotFinder::MIN_VALID_PIXELS) && (in_minus_mean > 0) && (tmp1 > tmp2);

    bool count_criterion = (params.count_threshold == 0.0f) || (val > params.count_threshold);

    bool strong_pixel = snr_criterion && count_criterion;
    if (val == INT32_MAX)
        strong_pixel = true;
    else if (val == INT32_MIN)
        strong_pixel = false;
    return strong_pixel ? 1 : 0;
}

// Inclusive prefix sum over the lanes of a warp (modular arithmetic).
__device__ __forceinline__ uint64_t warp_inclusive_scan(uint64_t v) {
    const int32_t lane = threadIdx.x & (WARP_SIZE - 1);
    for (int offset = 1; offset < WARP_SIZE; offset *= 2) {
        const uint64_t t = __shfl_up_sync(UINT32_MAX, v, offset);
        if (lane >= offset)
            v += t;
    }
    return v;
}

// Sum over the 2 * NBX + 1 = 31 columns of each lane's window, the columns held two per lane: a from
// lane i is column i of the warp's 64, b from lane i is column 32 + i (lane 31 holds no b). Lane l's
// window is columns l + 1 .. l + 31: a of lanes l+1..31 plus b of lanes 0..l-1.
__device__ __forceinline__ uint64_t warp_window_sum(uint64_t a, uint64_t b) {
    static_assert(2 * ImageSpotFinder::NBX + 1 == WARP_SIZE - 1, "the two-columns-per-lane layout needs a 31-pixel window");
    const int32_t lane = threadIdx.x & (WARP_SIZE - 1);
    const uint64_t pa = warp_inclusive_scan(a);
    const uint64_t pb = warp_inclusive_scan(b);
    const uint64_t total_a = __shfl_sync(UINT32_MAX, pa, WARP_SIZE - 1);
    uint64_t pb_before = __shfl_up_sync(UINT32_MAX, pb, 1);
    if (lane < 1)
        pb_before = 0;
    return total_a - pa + pb_before;
}

// Find pixels that could be spots
// in: image input values
// out: pixel result bit array, 1 bit per pixel (0:no/1:candidate spot)
// prev_out: result of a previous pass; its pixels read as INT32_MAX (not counted, and strong).
//           nullptr = no previous pass.
// needed: nullptr, or a bit buffer of the pixels whose result will actually be read by someone who
//         looks within NBX pixels of them (analyze_candidates). A warp whose tile holds no pixel that
//         any of them can reach leaves its tile unwritten.
// params: spot finding parameters
//
// One warp per 32 output columns and a band of rows (a "wave", gridDim-independent: the warps are
// numbered group-fastest). Each lane keeps the vertical sums (sum, sum2, count) of two input columns
// over the window's rows in registers - 64 columns for the warp, enough for 32 windows of 31 - and
// slides them one row at a time: the row leaving the window is read again from global memory (it was
// read 31 rows earlier and sits in cache) and the row entering it is added. The horizontal window
// sums come from warp prefix scans, so there is no shared memory and no block-wide synchronisation.
// All sums are integer (modular 64-bit), so the result is exact and independent of the order.
__global__ void analyze_pixel(const int32_t *in, const uint32_t *prev_out, uint32_t *out,
                              const uint32_t *needed, const spot_parameters params, int32_t nWaves)
{
    constexpr int32_t NBX = ImageSpotFinder::NBX;
    const int32_t lane = threadIdx.x & (WARP_SIZE - 1);
    const int32_t warp = (blockIdx.x * blockDim.x + threadIdx.x) / WARP_SIZE;
    const int32_t ngroups = (params.width + WARP_SIZE - 1) / WARP_SIZE;
    const int32_t group = warp % ngroups;
    const int32_t wave = warp / ngroups;
    const int32_t rowsPerWave = (params.height + nWaves - 1) / nWaves;
    const int32_t rmin = wave * rowsPerWave;
    const int32_t rmax = min(rmin + rowsPerWave, params.height);
    // Warp-uniform, so the shuffles and ballots below stay collective.
    if (wave >= nWaves || rmin >= params.height)
        return;

    const int32_t out_col = group * WARP_SIZE + lane;          // the column this lane writes
    const int32_t col_a = group * WARP_SIZE - NBX - 1 + lane;  // the two input columns this lane sums
    const int32_t col_b = col_a + WARP_SIZE;
    const bool use_a = col_a >= 0 && col_a < params.width;
    const bool use_b = lane < WARP_SIZE - 1 && col_b >= 0 && col_b < params.width;

    if (needed != nullptr) {
        // Is any needed pixel within NBX of the tile, rows [rmin, rmax) x columns [c0, c0 + 32)?
        // Each lane checks rows of the dilated band, the columns [c0 - NBX, c0 + 32 + NBX) as the
        // (at most three) words they fall in, masked to exactly that range.
        const int64_t c_lo = max(group * WARP_SIZE - NBX, 0);
        const int64_t c_hi = min(group * WARP_SIZE + WARP_SIZE + NBX, params.width);  // past the last
        bool any = false;
        for (int32_t r = max(rmin - NBX, 0) + lane; r < min(rmax + NBX, params.height) && !any; r += WARP_SIZE) {
            const int64_t first = static_cast<int64_t>(r) * params.width + c_lo;
            const int64_t last = static_cast<int64_t>(r) * params.width + c_hi - 1;
            for (int64_t w = first / 32; w <= last / 32; w++) {
                uint32_t bits = needed[w];
                if (w == first / 32)
                    bits &= UINT32_MAX << (first % 32);
                if (w == last / 32 && last % 32 != 31)
                    bits &= (1U << (last % 32 + 1)) - 1;
                any = any || (bits != 0);
            }
        }
        if (!__any_sync(UINT32_MAX, any))
            return;
    }

    const auto value_at = [&](int32_t row, int32_t col) -> int32_t {
        const int32_t npixel = row * params.width + col;
        const bool sat = prev_out != nullptr && ((prev_out[npixel / 32] & (1U << (npixel % 32))) != 0);
        return sat ? INT32_MAX : in[npixel];
    };

    uint64_t sum_a = 0, sum2_a = 0, count_a = 0;
    uint64_t sum_b = 0, sum2_b = 0, count_b = 0;
    // Add (sign +1) or remove (-1) row r of this lane's two columns; sentinels count as nothing.
    const auto slide = [&](int32_t row, uint64_t sign) {
        if (use_a) {
            const int32_t v = value_at(row, col_a);
            if (v != INT32_MAX && v != INT32_MIN) {
                sum_a += sign * static_cast<uint64_t>(static_cast<int64_t>(v));
                sum2_a += sign * static_cast<uint64_t>(static_cast<int64_t>(v) * v);
                count_a += sign;
            }
        }
        if (use_b) {
            const int32_t v = value_at(row, col_b);
            if (v != INT32_MAX && v != INT32_MIN) {
                sum_b += sign * static_cast<uint64_t>(static_cast<int64_t>(v));
                sum2_b += sign * static_cast<uint64_t>(static_cast<int64_t>(v) * v);
                count_b += sign;
            }
        }
    };

    for (int32_t r = max(rmin - NBX, 0); r < min(rmin + NBX, params.height - 1) + 1; r++)
        slide(r, 1);

    for (int32_t row = rmin; row < rmax; row++) {
        const auto sum = static_cast<int64_t>(warp_window_sum(sum_a, sum_b));
        const auto sum2 = static_cast<int64_t>(warp_window_sum(sum2_a, sum2_b));
        const auto count = static_cast<int64_t>(warp_window_sum(count_a, count_b));
        uint8_t val = 0;
        if (out_col < params.width)
            val = pixel_result(params, value_at(row, out_col), sum, sum2, count);
        write_result(params, out, row * params.width + out_col, val);

        if (row - NBX >= 0)
            slide(row - NBX, UINT64_MAX);          // -1: the row leaving the window
        if (row + NBX + 1 < params.height)
            slide(row + NBX + 1, 1);
    }
}

// The second pass of analyze_pixel, evaluated only at the candidate pixels (bit set in cand) instead
// of over the whole image. Used where the caller keeps only (pass-2 result & cand), as the adaptive
// finder does with its ring mask: every other pixel of the dense pass-2 result is discarded, and a
// pixel's pass-2 result depends only on the image and the pass-1 bits inside its own window, so this
// yields exactly those bits. The window is summed directly - the same clipped 31 x 31 box, the same
// exclusion of sentinel and pass-1 pixels, integer sums, the same pixel_result - so the result is
// bit-identical to the dense pass followed by the AND.
//
// One warp per candidate: lane dx (0..30) sums column c + dx - NBX over the window's rows, and the
// warp reduces. The candidate words are scanned 32 at a time, one per lane; a word is owned by one
// warp, which writes it whole, so out needs no atomics (it must be zeroed beforehand).
__global__ void analyze_candidates(const int32_t *in, const uint32_t *prev_out, const uint32_t *cand,
                                   uint32_t *out, const spot_parameters params, size_t nwords)
{
    constexpr unsigned ALL_THREADS = UINT32_MAX;
    constexpr int NBX = ImageSpotFinder::NBX;
    const int lane = threadIdx.x & (WARP_SIZE - 1);
    const size_t warp = (static_cast<size_t>(blockIdx.x) * blockDim.x + threadIdx.x) / WARP_SIZE;
    const size_t nwarps = static_cast<size_t>(gridDim.x) * blockDim.x / WARP_SIZE;
    const int32_t npix = params.width * params.height;

    const auto value_at = [&](int32_t pixel) -> int32_t {
        const bool sat = ((prev_out[pixel / 32] & (1U << (pixel % 32))) != 0);
        return sat ? INT32_MAX : in[pixel];
    };

    for (size_t base = warp * WARP_SIZE; base < nwords; base += nwarps * WARP_SIZE) {
        const uint32_t my_word = (base + lane < nwords) ? cand[base + lane] : 0;
        unsigned words = __ballot_sync(ALL_THREADS, my_word != 0);
        while (words) {
            const int src = __ffs(words) - 1;
            words &= words - 1;
            uint32_t bits = __shfl_sync(ALL_THREADS, my_word, src);
            const size_t word = base + src;
            uint32_t result = 0;
            while (bits) {
                const int b = __ffs(bits) - 1;
                bits &= bits - 1;
                const int32_t pixel = static_cast<int32_t>(word * 32 + b);
                if (pixel >= npix)
                    break;
                const int32_t row = pixel / params.width;
                const int32_t col = pixel % params.width + lane - NBX;

                int64_t sum = 0, sum2 = 0;
                int32_t count = 0;
                if (lane < 2 * NBX + 1 && col >= 0 && col < params.width) {
                    const int32_t rlo = max(row - NBX, 0);
                    const int32_t rhi = min(row + NBX, params.height - 1);
                    for (int32_t r = rlo; r <= rhi; r++) {
                        const int32_t val = value_at(r * params.width + col);
                        if (val != INT32_MAX && val != INT32_MIN) {
                            sum += val;
                            sum2 += static_cast<int64_t>(val) * val;
                            count += 1;
                        }
                    }
                }
                for (int offset = WARP_SIZE / 2; offset > 0; offset /= 2) {
                    sum += __shfl_down_sync(ALL_THREADS, sum, offset);
                    sum2 += __shfl_down_sync(ALL_THREADS, sum2, offset);
                    count += __shfl_down_sync(ALL_THREADS, count, offset);
                }
                if (lane == 0 && pixel_result(params, value_at(pixel), sum, sum2, count))
                    result |= 1u << b;
            }
            if (lane == 0)
                out[word] = result;
        }
    }
}

ImageSpotFinderGPU::ImageSpotFinderGPU(int32_t in_width, int32_t in_height,
                                       std::shared_ptr<CudaStream> in_stream)
    : ImageSpotFinder(in_width, in_height, false),
      stream(in_stream),
      extractor(in_width, in_height, std::move(in_stream)) {
    gpu_out_0 = CudaDevicePtr<uint32_t>(OutputSize());
    gpu_out_1 = CudaDevicePtr<uint32_t>(OutputSize());
    int device;
    cuda_err(cudaGetDevice(&device));
    int sm_count;
    cuda_err(cudaDeviceGetAttribute(&sm_count, cudaDevAttrMultiProcessorCount, device));
    candidateBlocks = 8 * sm_count;
}

void ImageSpotFinderGPU::SetResolutionMaskBits(const std::vector<uint32_t> &packed_mask) {
    ImageSpotFinder::SetResolutionMaskBits(packed_mask);
    extractor.SetResolutionMask(res_mask_bits);
}

const std::vector<DiffractionSpot> &ImageSpotFinderGPU::ExtractComponents(const ImagePreprocessorBuffer &image,
                                                                          const SpotFindingSettings &settings) {
    extractor.Extract(gpu_out_1, image.getGPUBuffer(), settings, components);
    return components;
}

void ImageSpotFinderGPU::Detect(const ImagePreprocessorBuffer &image, const SpotFindingSettings &settings) {
    RunDetect(image, settings, nullptr);
    // The bit buffer stays on the device - ExtractComponents reads it there.
    cuda_err(cudaStreamSynchronize(*stream));
}

void ImageSpotFinderGPU::DetectAt(const ImagePreprocessorBuffer &image, const SpotFindingSettings &settings,
                                  const uint32_t *gpu_candidates) {
    RunDetect(image, settings, gpu_candidates);
}

void ImageSpotFinderGPU::RunDetect(const ImagePreprocessorBuffer &image, const SpotFindingSettings &settings,
                                   const uint32_t *gpu_candidates) {
    spot_parameters spot_params{};
    spot_params.height = height;
    spot_params.width = width;
    spot_params.strong_pixel_threshold2 = settings.signal_to_noise_threshold * settings.signal_to_noise_threshold;
    spot_params.count_threshold = settings.photon_count_threshold;

    if (2 * NBX + 1 > windowSizeLimit)
        throw JFJochException(JFJochExceptionCategory::SpotFinderError, "nbx exceeds window size limit");
    if (2 * NBX + 1 > windowSizeLimit)
        throw JFJochException(JFJochExceptionCategory::SpotFinderError, "nby exceeds window size limit");
    if (windowSizeLimit > numberOfCudaThreads)
        throw JFJochException(JFJochExceptionCategory::SpotFinderError, "window size limit exceeds number of cuda threads");
    if (windowSizeLimit > spot_params.width)
        throw JFJochException(JFJochExceptionCategory::SpotFinderError, "window size limit exceeds number of columns");
    if (windowSizeLimit > spot_params.height)
        throw JFJochException(JFJochExceptionCategory::SpotFinderError, "window size limit exceeds number of height");

    const int32_t ngroups = (spot_params.width + 31) / 32;
    const int32_t warpsPerBlock = numberOfCudaThreads / 32;
    const int32_t nBlocks = (ngroups * numberOfWaves + warpsPerBlock - 1) / warpsPerBlock;

    cuda_err(cudaMemsetAsync(gpu_out_0, 0, OutputSize() * sizeof(uint32_t), *stream));
    cuda_err(cudaMemsetAsync(gpu_out_1, 0, OutputSize() * sizeof(uint32_t), *stream));
    // The first pass has no previous one (the classic engine used to hand it the zeroed gpu_out_1).
    analyze_pixel<<<nBlocks, numberOfCudaThreads, 0, *stream>>>
            (image.getGPUBuffer(), nullptr, gpu_out_0, gpu_candidates, spot_params, numberOfWaves);
    cuda_err(cudaGetLastError());
    if (gpu_candidates == nullptr)
        analyze_pixel<<<nBlocks, numberOfCudaThreads, 0, *stream>>>
                (image.getGPUBuffer(), gpu_out_0, gpu_out_1, nullptr, spot_params, numberOfWaves);
    else
        analyze_candidates<<<candidateBlocks, 256, 0, *stream>>>
                (image.getGPUBuffer(), gpu_out_0, gpu_candidates, gpu_out_1, spot_params, OutputSize());
    cuda_err(cudaGetLastError());
}