Jungfraujoch/preview/PreviewImage.cpp

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

#include <algorithm>
#include <cmath>
#include <future>
#include <optional>
#include <thread>

#include "PreviewImage.h"

#include "JFJochJPEG.h"
#include "JFJochTIFF.h"
#include "../common/JFJochException.h"
#include "../common/JFJochMath.h"
#include "../common/ThreadAffinity.h"
#include "../common/DiffractionGeometry.h"
#include "../frame_serialize/CBORStream2Deserializer.h"
#include "../compression/JFJochDecompress.h"
#include "../image_analysis/bragg_integration/SystematicAbsence.h"

constexpr const static rgb lime = {.r = 0xcd, .g = 0xdc, .b = 0x39};
constexpr const static rgb pink = {.r = 0xe9, .g = 0x1e, .b = 0x63};

constexpr const static rgb purple = {.r = 0x7b, .g = 0x1f, .b = 0xA2};
constexpr const static rgb orange = {.r = 0xff, .g = 0x57, .b = 0x22};
constexpr const static rgb amber = {.r =0xff, .g = 0xc1, .b = 0x07};
constexpr const static rgb blue = {.r = 0x0d, .g = 0x47, .b = 0xa1};
constexpr const static rgb cyan = {.r = 0x00, .g = 0xff, .b = 0xff}; // "ice" color

// Spot/prediction overlay palette, matching the jfjoch_viewer diffraction image so the two
// front-ends look identical: green = not indexed, magenta = indexed (primary lattice),
// cyan = on an ice ring, coral = secondary/further lattice, dark red = Bragg prediction.
constexpr const static rgb green = {.r = 0x00, .g = 0xff, .b = 0x00};
constexpr const static rgb magenta = {.r = 0xff, .g = 0x00, .b = 0xff};
constexpr const static rgb coral = {.r = 0xfa, .g = 0x72, .b = 0x68};
constexpr const static rgb dark_red = {.r = 0x80, .g = 0x00, .b = 0x00};

constexpr const static rgb plotly[] = {{0x1f, 0x77, 0xb4},
                                       {0xff, 0x7f, 0x0e},
                                       {0x2c, 0xa0, 0x2c},
                                       {0xd6, 0x27, 0x28},
                                       {0x94, 0x67, 0xbd},
                                       {0x8c, 0x56, 0x4b},
                                       {0xe3, 0x77, 0xc2},
                                       {0x7f, 0x7f, 0x7f},
                                       {0xbd, 0xbd, 0x22},
                                       {0x17, 0xbe, 0xcf}};

constexpr const static rgb gray = {.r = 0xbe, .g = 0xbe, .b = 0xbe};

void PreviewImage::color_pixel(std::vector<rgb> &ret, int64_t in_xpixel, int64_t in_ypixel,const rgb &color) const {
    if ((in_xpixel >= 0) && (in_xpixel < xpixel) && (in_ypixel >= 0) && (in_ypixel < ypixel))
        ret[(in_ypixel * xpixel + in_xpixel)] = color;
}

void PreviewImage::spot(std::vector<rgb> &ret, int64_t in_xpixel, int64_t in_ypixel, const rgb &color) const {
        color_pixel(ret, in_xpixel, in_ypixel, color);
}

void PreviewImage::roi(std::vector<rgb> &ret, int64_t in_xpixel, int64_t in_ypixel, int64_t roi_number) const {
    color_pixel(ret, in_xpixel, in_ypixel, plotly[roi_number % 10]);
}
template<class T>
std::vector<rgb> PreviewImage::GenerateRGB(const uint8_t *value_8,
                                           int64_t special_value_64,
                                           int64_t sat_value_64,
                                           const ColorScale &scale,
                                           const PreviewImageSettings &settings) const {
    auto value = reinterpret_cast<const T *>(value_8);
    auto special_value = static_cast<T>(special_value_64);

    float background = settings.background_value.value_or(0.0);
    float foreground;
    if (settings.saturation_value.has_value())
        foreground = settings.saturation_value.value();
    else {
        // Auto-contrast procedure
        std::vector<int64_t> valid;
        valid.reserve(xpixel * ypixel);
        for (int i = 0; i < xpixel * ypixel; i++) {
            if ((value[i] != special_value)
                && (value[i] != sat_value_64)
                && (mask[i] != MaskDet)
                && (mask[i] != MaskGap)
                && (!settings.show_user_mask || (mask[i] != MaskUsr)))
                valid.push_back(static_cast<int64_t>(value[i]));
        }

        if (!valid.empty()) {
            const size_t m = valid.size();
            size_t ignore = std::max<size_t>(1, static_cast<size_t>(std::floor(m * auto_foreground_range)));
            if (ignore >= m) ignore = m - 1; // ensure at least one value remains
            const size_t rank = m - ignore - 1; // 0-based index for the desired value
            std::nth_element(valid.begin(), valid.begin() + rank, valid.end());
            foreground = static_cast<float>(valid[rank]);
        } else {
            // Fallback to something above background if no valid pixels remain
            foreground = background + 1.0f;
        }

    }

    // LUT-based mapping (fast path)
    const auto &lut = scale.LUTData();
    const int64_t lut_size = static_cast<int64_t>(lut.size());
    const float lut_scale = static_cast<float>(lut_size - 1);
    const float inv_range = (foreground > background)
        ? (lut_scale / (foreground - background))
        : 0.0f;

    const rgb gap_color = scale.Apply(ColorScaleSpecial::Gap);
    const rgb bad_color = scale.Apply(ColorScaleSpecial::BadPixel);

    std::vector<rgb> ret(xpixel * ypixel);
    for (int i = 0; i < xpixel * ypixel; i++) {
        if (mask[i] == MaskGap) {
            ret[i] = gap_color;
        } else if ((value[i] == special_value)
                   || (mask[i] == MaskDet)
                   || (settings.show_user_mask && (mask[i] == MaskUsr))) {
            ret[i] = bad_color;
        } else {
            const float v = static_cast<float>(value[i]);
            int64_t idx = static_cast<int64_t>((v - background) * inv_range + 0.5f);
            if (idx < 0) idx = 0;
            else if (idx >= lut_size) idx = lut_size - 1;
            ret[i] = lut[idx];
        }
    }
    return ret;
}

void PreviewImage::AddBeamCenter(std::vector<rgb> &rgb_image) const {
    // The true direct beam is where the primary beam hits the detector, which differs from the
    // stored beam origin (PONI) whenever the detector is tilted.
    auto [bx, by] = experiment.GetDiffractionGeometry().GetDirectBeam_pxl();
    if (!std::isfinite(bx) || !std::isfinite(by))
        return;
    int64_t beam_x_int = std::lround(bx);
    int64_t beam_y_int = std::lround(by);

    int crosshair_size = 30;
    int crosshair_width = 3;
    for (int w = -crosshair_width; w <= crosshair_width; w++) {
        for (int i = -crosshair_size; i <= crosshair_size; i++) {
            color_pixel(rgb_image, beam_x_int + i, beam_y_int + w, lime);
            color_pixel(rgb_image, beam_x_int + w, beam_y_int + i, lime);
        }
    }
}

void PreviewImage::AddSpots(std::vector<rgb> &rgb_image,
                            const std::vector<SpotToSave>& in_spots) const {
    for (const auto &s: in_spots) {
        int64_t spot_x_int = std::lround(s.x);
        int64_t spot_y_int = std::lround(s.y);

        int rectangle_size = 4;
        int rectangle_width = 3;

        rgb color = green;                                   // not indexed
        if (s.indexed)
            color = (s.lattice >= 1) ? coral : magenta;      // secondary lattice vs primary
        else if (s.ice_ring)
            color = cyan;

        for (int z = rectangle_size; z < rectangle_size + rectangle_width; z++) {
            for (int w = -z; w <= z; w++) {
                spot(rgb_image, spot_x_int + z, spot_y_int + w, color);
                spot(rgb_image, spot_x_int - z, spot_y_int + w, color);
                spot(rgb_image, spot_x_int + w, spot_y_int + z, color);
                spot(rgb_image, spot_x_int + w, spot_y_int - z, color);
            }
        }
    }
}

void PreviewImage::AddROI(std::vector<rgb> &rgb_image) const {
    int64_t roi_counter = 0;

    for (const auto &box: experiment.ROI().GetROIDefinition().boxes) {
        int rectangle_width = 5;

        for (auto x = box.GetXMin() - rectangle_width; x <= box.GetXMax() + rectangle_width; x++) {
            for (auto w = 1; w <= rectangle_width; w++) {
                roi(rgb_image, x, box.GetYMax() + w, roi_counter);
                roi(rgb_image, x, box.GetYMin() - w, roi_counter);
            }
        }

        for (auto y = box.GetYMin() - rectangle_width; y <= box.GetYMax() + rectangle_width; y++) {
            for (auto w = 1; w <= rectangle_width; w++) {
                roi(rgb_image, box.GetXMax() + w, y, roi_counter);
                roi(rgb_image, box.GetXMin() - w, y, roi_counter);
            }
        }
        roi_counter++;
    }

    for (const auto &circle: experiment.ROI().GetROIDefinition().circles) {
        int width = 5;

        for (int64_t y = std::floor(circle.GetY() - circle.GetRadius_pxl() - width);
             y <= std::ceil(circle.GetY() + circle.GetRadius_pxl() + width);
             y++) {
            for (int64_t x = std::floor(circle.GetX() - circle.GetRadius_pxl() - width);
                 x <= std::ceil(circle.GetX() + circle.GetRadius_pxl() + width);
                 x++) {
                    float dist = sqrtf((x - circle.GetX()) * (x - circle.GetX())
                        + (y - circle.GetY()) * (y - circle.GetY()));

                    if ((dist > circle.GetRadius_pxl()) && (dist < circle.GetRadius_pxl() + width))
                        roi(rgb_image, x, y, roi_counter);
            }
        }
        roi_counter++;
    }

    DiffractionGeometry geom = experiment.GetDiffractionGeometry();
    for (const auto &az: experiment.ROI().GetROIDefinition().azimuthal) {
        const rgb color = plotly[roi_counter % 10];
        const float d_inner = az.GetDMax_A();   // larger d -> smaller radius (inner arc)
        const float d_outer = az.GetDMin_A();   // smaller d -> larger radius (outer arc)
        constexpr float deg2rad = static_cast<float>(PI) / 180.0f;

        if (az.HasPhi()) {
            float phi0 = az.GetPhiMin_deg() * deg2rad;
            float phi1 = az.GetPhiMax_deg() * deg2rad;
            if (phi1 < phi0)
                phi1 += 2.0f * static_cast<float>(PI);   // unwrap a sector that crosses 0

            DrawArc(rgb_image, geom, d_outer, phi0, phi1, color, 2);
            DrawArc(rgb_image, geom, d_inner, phi0, phi1, color, 2);

            // Straight radial edges joining the inner and outer arc at each sector limit.
            auto radial_edge = [&](float phi) {
                try {
                    auto [ax, ay] = geom.ResPhiToPxl(d_outer, phi);
                    auto [bx, by] = geom.ResPhiToPxl(d_inner, phi);
                    if (std::isfinite(ax) && std::isfinite(ay) && std::isfinite(bx) && std::isfinite(by))
                        DrawThickLine(rgb_image, ax, ay, bx, by, color, 2);
                } catch (...) {}
            };
            radial_edge(phi0);
            radial_edge(phi1);
        } else {
            const float two_pi = 2.0f * static_cast<float>(PI);
            DrawArc(rgb_image, geom, d_outer, 0.0f, two_pi, color, 2);
            DrawArc(rgb_image, geom, d_inner, 0.0f, two_pi, color, 2);
        }
        roi_counter++;
    }
}

void PreviewImage::AddResolutionRing(std::vector<rgb> &rgb_image, float d) const {
    DrawArc(rgb_image, experiment.GetDiffractionGeometry(), d, 0.0f, 2.0f * static_cast<float>(PI), orange, 1);
}

void PreviewImage::DrawThickLine(std::vector<rgb> &rgb_image, float x0, float y0, float x1, float y1,
                                 const rgb &color, int halfwidth) const {
    const float dx = x1 - x0, dy = y1 - y0;
    int n = static_cast<int>(std::ceil(std::max(std::fabs(dx), std::fabs(dy))));
    if (n < 1) n = 1;
    for (int i = 0; i <= n; i++) {
        const float t = static_cast<float>(i) / static_cast<float>(n);
        const int64_t px = std::lround(x0 + t * dx);
        const int64_t py = std::lround(y0 + t * dy);
        for (int a = -halfwidth; a <= halfwidth; a++)
            for (int b = -halfwidth; b <= halfwidth; b++)
                color_pixel(rgb_image, px + a, py + b, color);
    }
}

void PreviewImage::DrawArc(std::vector<rgb> &rgb_image, const DiffractionGeometry &geom, float d,
                          float phi_start, float phi_end, const rgb &color, int halfwidth) const {
    // Sample the constant-d arc finely enough that neighbouring samples stay a few pixels apart,
    // then join them with straight segments. ResPhiToPxl carries the detector tilt, so this traces
    // the true conic instead of a PONI-centred circle. It throws when d is too high for the
    // wavelength, and returns NaN where the contour leaves the detector plane - break there.
    const float r_est = geom.ResToPxl(d);
    const float span = std::fabs(phi_end - phi_start);
    const int steps = std::clamp<int>(static_cast<int>(std::lround(std::fabs(r_est) * span * 0.5f)), 60, 8192);
    std::optional<std::pair<float, float>> prev;
    for (int i = 0; i <= steps; i++) {
        const float phi = phi_start + (phi_end - phi_start) * static_cast<float>(i) / static_cast<float>(steps);
        std::pair<float, float> pt;
        try {
            pt = geom.ResPhiToPxl(d, phi);
        } catch (...) {
            return;   // d too high for the wavelength - nothing to draw
        }
        if (!std::isfinite(pt.first) || !std::isfinite(pt.second)) {
            prev.reset();
            continue;
        }
        if (prev)
            DrawThickLine(rgb_image, prev->first, prev->second, pt.first, pt.second, color, halfwidth);
        prev = pt;
    }
}

void PreviewImage::DrawCircleOutline(std::vector<rgb> &rgb_image, float cx, float cy, float radius,
                                     int width, const rgb &color) const {
    const int64_t x_lo = std::floor(cx - radius - width);
    const int64_t x_hi = std::ceil(cx + radius + width);
    const int64_t y_lo = std::floor(cy - radius - width);
    const int64_t y_hi = std::ceil(cy + radius + width);
    for (int64_t y = y_lo; y <= y_hi; y++) {
        for (int64_t x = x_lo; x <= x_hi; x++) {
            const float dist = std::sqrt((x - cx) * (x - cx) + (y - cy) * (y - cy));
            if (dist >= radius && dist <= radius + width)
                color_pixel(rgb_image, x, y, color);
        }
    }
}

void PreviewImage::AddPredictions(std::vector<rgb> &rgb_image, const std::vector<Reflection> &reflections,
                                  char centering) const {
    // Draw predictions as dark-red circles (spots are squares), matching the viewer overlay.
    // Reflections absent under the lattice centering are integrated but not real predictions - skip them.
    for (const auto &s : reflections) {
        if (systematic_absence(s.h, s.k, s.l, centering))
            continue;
        DrawCircleOutline(rgb_image, s.predicted_x, s.predicted_y, 5.0f, 2, dark_red);
    }
}

void PreviewImage::ConfigurePixel(const std::vector<uint32_t> &mask_tmp, size_t pixel_begin, size_t pixel_end) {
    constexpr uint32_t gap_bits =
        (1u << PixelMask::ModuleGapPixelBit)
        | (1u << PixelMask::ChipGapPixelBit)
        | (1u << PixelMask::ModuleEdgePixelBit);

    // Bits 1-7 and 10-15. The beam-stop shadow (bit 9) is a deliberate exclusion rather than
    // a detector defect, so it is shown the same way as the user mask.
    constexpr uint32_t det_bits = 0xFCFEu;
    constexpr uint32_t usr_bits = (1u << PixelMask::UserMaskedPixelBit)
                                | (1u << PixelMask::BeamStopPixelBit);

    for (size_t i = pixel_begin; i < pixel_end; i++) {
        const auto pixel_val = mask_tmp[i];

        if (pixel_val == 0)
            mask[i] = 0;
        else if ((pixel_val & gap_bits) != 0)
            mask[i] = MaskGap;
        else if ((pixel_val & det_bits) != 0)
            mask[i] = MaskDet;
        else if ((pixel_val & usr_bits) != 0)
            mask[i] = MaskUsr;
        else
            mask[i] = 0;
    }
}

void PreviewImage::Configure(const DiffractionExperiment &in_experiment, const PixelMask &pixel_mask, size_t nthreads) {
    std::unique_lock ul(m);

    experiment = in_experiment;
    xpixel = experiment.GetXPixelsNum();
    ypixel = experiment.GetYPixelsNum();
    pixel_depth_bytes = experiment.GetByteDepthImage();
    pixel_is_signed = experiment.IsPixelSigned();

    mask.resize(experiment.GetPixelsNum(), 0);

    if (nthreads == 0)
        nthreads = AvailableCpus();

    nthreads = std::clamp<size_t>(nthreads, 1, 8);

    auto &mask_tmp = pixel_mask.GetMask(experiment);

    std::vector<std::future<void> > futures;
    futures.reserve(nthreads);

    size_t npixel = experiment.GetPixelsNum();

    for (size_t t = 0; t < nthreads; ++t)
        futures.emplace_back(std::async(std::launch::async,
                                        &PreviewImage::ConfigurePixel, this, std::cref(mask_tmp),
                                        t * npixel / nthreads,
                                        (t + 1) * npixel / nthreads));

    for (auto &f: futures)
        f.get();
}

std::vector<rgb> PreviewImage::GenerateRGB(const PreviewImageSettings &settings, const DataMessage &msg) const {
    std::vector<rgb> v(msg.image.GetWidth() * msg.image.GetHeight());
    if (msg.image.GetUncompressedSize() == 0)
        return {};

    std::vector<uint8_t> tmp;
    const uint8_t* image_ptr = msg.image.GetUncompressedPtr(tmp);

    {
        // JPEG compression is outside the critical loop protected by m
        std::unique_lock ul(m);

        ColorScale scale;
        scale.Select(settings.scale);

        switch (msg.image.GetMode()) {
            case CompressedImageMode::Int8:
                v = GenerateRGB<int8_t>(image_ptr, INT8_MIN, INT8_MAX, scale, settings);
                break;
            case CompressedImageMode::Int16:
                v = GenerateRGB<int16_t>(image_ptr, INT16_MIN, INT16_MAX, scale, settings);
                break;
            case CompressedImageMode::Int32:
                v = GenerateRGB<int32_t>(image_ptr, INT32_MIN, INT32_MAX, scale, settings);
                break;
            case CompressedImageMode::Uint8:
                v = GenerateRGB<uint8_t>(image_ptr,UINT8_MAX, UINT8_MAX, scale, settings);
                break;
            case CompressedImageMode::Uint16:
                v = GenerateRGB<uint16_t>(image_ptr,UINT16_MAX, UINT16_MAX, scale, settings);
                break;
            case CompressedImageMode::Uint32:
                v = GenerateRGB<uint32_t>(image_ptr,UINT32_MAX, UINT32_MAX, scale, settings);
                break;
            default:
                throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Mode not supported");
        }

        if (settings.show_spots)
            AddSpots(v, msg.spots);

        if (settings.show_predictions) {
            const char centering = msg.lattice_type.has_value() ? msg.lattice_type->centering : 'P';
            AddPredictions(v, msg.reflections, centering);
        }

        if (settings.show_roi)
            AddROI(v);

        if (settings.resolution_ring)
            AddResolutionRing(v, settings.resolution_ring.value());
        else if (settings.show_res_est && msg.resolution_estimate)
            AddResolutionRing(v, msg.resolution_estimate.value());

        if (settings.show_beam_center)
            AddBeamCenter(v);
    }
    return v;
}

std::string PreviewImage::GenerateImage(const PreviewImageSettings& settings, const DataMessage &msg) const {
    auto v = GenerateRGB(settings, msg);
    CompressedImage rgb_image(v, msg.image.GetWidth(), msg.image.GetHeight());
    switch (settings.format) {
        case PreviewImageFormat::JPEG:
            return WriteJPEGToMem(rgb_image, settings.jpeg_quality);
        case PreviewImageFormat::TIFF:
            return WriteTIFFToString(rgb_image);
        default:
            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                  "Preview image format not supported");
    }
}

std::string PreviewImage::GenerateImage(const PreviewImageSettings &settings, const std::vector<uint8_t> &cbor_format) {
    auto cbor = CBORStream2Deserialize(cbor_format);
    if (!cbor || !cbor->data_message)
        return {};

    return GenerateImage(settings, *cbor->data_message);
}

std::string PreviewImage::GenerateTIFF(const std::vector<uint8_t>& cbor_format) {
    auto cbor = CBORStream2Deserialize(cbor_format);
    if (!cbor || !cbor->data_message)
        return {};

    return WriteTIFFToString(cbor->data_message->image);
}