Jungfraujoch/common/PixelMask.cpp

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

#include "PixelMask.h"
#include "RawToConvertedGeometry.h"
#include "TableChecksum.h"
#include "JFJochException.h"
#include "JFJochCompressor.h"

PixelMask::PixelMask() = default;

PixelMask::PixelMask(size_t width, size_t height)
        : mask(width*height, 0) {
    UpdateBinaryMask();
}

PixelMask::PixelMask(const DiffractionExperiment &experiment)
        : PixelMask(experiment.GetXPixelsNumConv(),
                    experiment.GetYPixelsNumConv()) {
    CalcEdgePixels(experiment);
}

PixelMask::PixelMask(const std::vector<uint32_t> &in_mask) : mask(in_mask) {
    UpdateBinaryMask();
}

uint32_t PixelMask::LoadMask(const std::vector<uint32_t> &input_mask, uint8_t bit) {
    uint32_t ret = 0;
    if (input_mask.size() != mask.size())
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "Input match doesn't fit the detector ");

    for (int i = 0; i < mask.size(); i++) {
        if (input_mask[i] != 0) {
            mask[i] |= (1 << bit);
            ret++;
        } else
            mask[i] &= ~(1 << bit);
    }
    return ret;
}

void PixelMask::UpdateDerived(const DiffractionExperiment &experiment) {
    switch (experiment.GetDetectorType()) {
        case DetectorType::JUNGFRAU:
        case DetectorType::EIGER:
            raw_mask.resize(experiment.GetModulesNum() * RAW_MODULE_SIZE, 0);
            ConvertedToRawGeometry(experiment, raw_mask.data(), mask.data());
            break;
        default:
            raw_mask.clear();
            break;
    }
    UpdateBinaryMask();
}

void PixelMask::UpdateBinaryMask() {
    binary_mask.resize(mask.size());
    for (size_t i = 0; i < mask.size(); i++)
        binary_mask[i] = (mask[i] != 0);
    binary_mask_checksum = TableChecksum(binary_mask.data(), binary_mask.size());
    packed_mask.assign((mask.size() + 31) / 32, 0);
    for (size_t i = 0; i < mask.size(); i++)
        packed_mask[i / 32] |= static_cast<uint32_t>(binary_mask[i]) << (i % 32);
}

void PixelMask::CalcEdgePixels_i(const DiffractionExperiment &experiment) {
    if (experiment.GetDetectorType() == DetectorType::DECTRIS)
        return;

    size_t nmodules = experiment.GetModulesNum();
    auto settings = experiment.GetImageFormatSettings();

    // Set module gaps to 1
    std::vector<uint32_t> module_gaps(nmodules * RAW_MODULE_SIZE, 0);
    std::vector<uint32_t> module_gaps_conv(experiment.GetPixelsNumConv(), 1);
    RawToConvertedGeometry(experiment, module_gaps_conv.data(), module_gaps.data());
    LoadMask(module_gaps_conv, ModuleGapPixelBit);

    // Calculate module edges and chip edges
    std::vector<uint32_t> module_edge(nmodules * RAW_MODULE_SIZE, 0);
    std::vector<uint32_t> chip_edge(nmodules * RAW_MODULE_SIZE, 0);
    for (int64_t module = 0; module < nmodules; module++) {
        for (int64_t line = 0; line < RAW_MODULE_LINES; line++) {
            for (int64_t col = 0; col < RAW_MODULE_COLS; col++) {
                int64_t pixel = module * RAW_MODULE_SIZE + line * RAW_MODULE_COLS + col;
                if ((line == 0)
                    || (line == RAW_MODULE_LINES - 1)
                    || (col == 0)
                    || (col == RAW_MODULE_COLS - 1))
                    module_edge[pixel] = 1;

                if ((col == 255) || (col == 256)
                    || (col == 511) || (col == 512)
                    || (col == 767) || (col == 768)
                    || (line == 255) || (line == 256))
                    chip_edge[pixel] = 1;
            }
        }
    }

    std::vector<uint32_t> module_edge_conv(experiment.GetPixelsNumConv(), 0);
    if (experiment.GetMaskModuleEdges())
        RawToConvertedGeometry(experiment, module_edge_conv.data(), module_edge.data());
    LoadMask(module_edge_conv, ModuleEdgePixelBit);

    std::vector<uint32_t> chip_edge_conv(experiment.GetPixelsNumConv(), 0);
    if (experiment.GetMaskChipEdges())
        RawToConvertedGeometry(experiment, chip_edge_conv.data(), chip_edge.data());
    LoadMask(chip_edge_conv, ChipGapPixelBit);
}

void PixelMask::CalcEdgePixels(const DiffractionExperiment &experiment)  {
    CalcEdgePixels_i(experiment);
    UpdateDerived(experiment);
}

const std::vector<uint32_t> &PixelMask::GetMaskRaw() const {
    if (raw_mask.empty())
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
            "Raw format not available for this detector");
    return raw_mask;
}

const std::vector<uint32_t> &PixelMask::GetMask() const {
    return mask;
}

const std::vector<uint8_t> &PixelMask::GetBinaryMask() const {
    return binary_mask;
}

const std::vector<uint32_t> &PixelMask::GetPackedMask() const {
    return packed_mask;
}

uint64_t PixelMask::GetBinaryMaskChecksum() const {
    return binary_mask_checksum;
}

const std::vector<uint32_t> &PixelMask::GetMask(const DiffractionExperiment& experiment) const {
    if (experiment.IsGeometryTransformed())
        return GetMask();
    else
        return GetMaskRaw();
}

std::vector<uint32_t> PixelMask::GetUserMask() const {
    std::vector<uint32_t> ret = GetMask();
    for (auto &i: ret)
        i = ((i & (1 << UserMaskedPixelBit)) != 0) ? 1 : 0;
    return ret;
}

std::vector<uint32_t> PixelMask::GetUserMask(const DiffractionExperiment& experiment) const {
    if (experiment.IsGeometryTransformed())
        return GetUserMask();
    else {
        std::vector<uint32_t> tmp = GetUserMask();
        std::vector<uint32_t> ret(experiment.GetModulesNum() * RAW_MODULE_SIZE, 0);
        ConvertedToRawGeometry(experiment, ret.data(), tmp.data());
        return ret;
    }
}


void PixelMask::LoadDetectorBadPixelMask(const DiffractionExperiment &experiment, const JFCalibration *calib) {
    if (experiment.GetDetectorType() == DetectorType::DECTRIS)
        return;

    std::vector<uint32_t> input_mask(experiment.GetModulesNum() * RAW_MODULE_SIZE, 0);
    std::vector<uint32_t> input_mask_rms(experiment.GetModulesNum() * RAW_MODULE_SIZE, 0);

    if (calib != nullptr) {
        for (int sc = 0; sc < experiment.GetStorageCellNumber(); sc++) {
            // For multiple SC PixelMask is logical sum of all image masks
            // (this can be too much, but better than too little)
            auto pedestal_g0 = calib->GetPedestal(0, sc);
            auto pedestal_g0_rms = calib->GetPedestalRMS(0, sc);
            auto pedestal_g1 = calib->GetPedestal(1, sc);
            auto pedestal_g2 = calib->GetPedestal(2, sc);

            for (int i = 0; i < experiment.GetModulesNum() * RAW_MODULE_SIZE; i++) {
                if (pedestal_g1[i] > 16383)
                    input_mask[i] = 1;
                if (!experiment.IsFixedGainG1()) {
                    if (pedestal_g0[i] >= 16383) {
                        if (experiment.IsMaskPixelsWithoutG0())
                            input_mask[i] = 1;
                    } else if (pedestal_g0_rms[i] > experiment.GetImageFormatSettings().GetPedestalG0RMSLimit())
                        input_mask_rms[i] = 1;

                    if (pedestal_g2[i] >= 16383)
                        input_mask[i] = 1;
                }
            }
        }
    }

    std::vector<uint32_t> input_mask_conv(experiment.GetPixelsNumConv(), 0);
    RawToConvertedGeometry(experiment, input_mask_conv.data(), input_mask.data());

    std::vector<uint32_t> input_mask_rms_conv(experiment.GetPixelsNumConv(), 0);
    RawToConvertedGeometry(experiment, input_mask_rms_conv.data(), input_mask_rms.data());

    LoadMask(input_mask_conv, ErrorPixelBit);
    LoadMask(input_mask_rms_conv, NoisyPixelBit);

    CalcEdgePixels_i(experiment);

    UpdateDerived(experiment);
}

PixelMaskStatistics PixelMask::GetStatistics() const {
    PixelMaskStatistics ret{};
    for (const auto &i: mask) {
        if (i & (1 << ModuleGapPixelBit))
            ret.module_gap_pixel++;
        else {
            if (i != 0)
                ret.total_masked++;
            if (i & (1 << ErrorPixelBit))
                ret.error_pixel++;
            if (i & (1 << NoisyPixelBit))
                ret.noisy_pixel++;
            if (i & (1 << UserMaskedPixelBit))
                ret.user_mask++;
            if (i & ((1 << ChipGapPixelBit) | (1 << ModuleEdgePixelBit)))
                ret.chip_gap_pixel++;
        }
    }
    return ret;
}

void PixelMask::LoadUserMask(const DiffractionExperiment& experiment, const std::vector<uint32_t> &in_mask) {
    if (in_mask.size() == mask.size()) {
        LoadMask(in_mask, UserMaskedPixelBit);
        UpdateDerived(experiment);
    } else if (in_mask.size() == experiment.GetModulesNum() * RAW_MODULE_SIZE) {
        std::vector<uint32_t> tmp(experiment.GetPixelsNumConv(), 0);
        RawToConvertedGeometry(experiment, tmp.data(), in_mask. data());
        LoadMask(tmp, UserMaskedPixelBit);
        UpdateDerived(experiment);
    } else
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "Size of input user mask invalid");
}

void PixelMask::LoadBeamStopMask(const DiffractionExperiment& experiment, const std::vector<uint32_t> &in_mask) {
    if (in_mask.size() != mask.size())
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "Size of input beam stop mask invalid");
    LoadMask(in_mask, BeamStopPixelBit);
    UpdateDerived(experiment);
}

void PixelMask::LoadHotPixelMask(const DiffractionExperiment& experiment, const std::vector<uint32_t> &in_mask) {
    if (in_mask.size() != mask.size())
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "Size of input hot pixel mask invalid");
    LoadMask(in_mask, HotPixelBit);
    UpdateDerived(experiment);
}

void PixelMask::ClearBeamStopMask(const DiffractionExperiment& experiment) {
    for (auto &i: mask)
        i &= ~(1u << BeamStopPixelBit);
    UpdateDerived(experiment);
}

void PixelMask::LoadUserMask(const DiffractionExperiment& experiment, const CompressedImage& image) {
    const size_t width = image.GetWidth();
    const size_t height = image.GetHeight();

    // The image has to match one of the two layouts handled by the vector
    // overload below: converted geometry, or raw stacked modules.
    const bool converted = (width == static_cast<size_t>(experiment.GetXPixelsNumConv()))
                           && (height == static_cast<size_t>(experiment.GetYPixelsNumConv()));
    const bool raw = (width == static_cast<size_t>(RAW_MODULE_COLS))
                     && (height == static_cast<size_t>(RAW_MODULE_LINES * experiment.GetModulesNum()));
    if (!converted && !raw)
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "User mask image size doesn't match the detector");

    std::vector<uint8_t> buffer;
    const uint8_t *bytes = image.GetUncompressedPtr(buffer);

    // A pixel is masked when its value is non-zero. Read each pixel as an
    // unsigned integer of the matching width - the sign is irrelevant when
    // comparing against zero.
    std::vector<uint32_t> mask(width * height);
    auto binarize = [&](auto sample) {
        using sample_t = decltype(sample);
        const auto *typed = reinterpret_cast<const sample_t *>(bytes);
        for (size_t i = 0; i < mask.size(); i++)
            mask[i] = (typed[i] != 0) ? 1 : 0;
    };

    switch (image.GetMode()) {
        case CompressedImageMode::Uint8:
        case CompressedImageMode::Int8:
            binarize(uint8_t{});
            break;
        case CompressedImageMode::Uint16:
        case CompressedImageMode::Int16:
            binarize(uint16_t{});
            break;
        case CompressedImageMode::Uint32:
        case CompressedImageMode::Int32:
            binarize(uint32_t{});
            break;
        default:
            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                                  "User mask must be an 8-, 16- or 32-bit integer image");
    }

    LoadUserMask(experiment, mask);
}

void PixelMask::LoadDECTRISBadPixelMask(const std::vector<uint32_t> &input_mask)  {
    if (input_mask.size() != mask.size())
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "Input match doesn't fit the detector ");

    uint32_t user_bitmask = (1 << UserMaskedPixelBit);
    uint32_t bad_pixel_bitmask = ~((1 << UserMaskedPixelBit) | (1 << ModuleGapPixelBit) | (1 << ChipGapPixelBit));

    for (int i = 0; i < mask.size(); i++) {
        if ((input_mask[i] & (1 << ModuleGapPixelBit)) != 0) {
            mask[i] = (1 << ModuleGapPixelBit);
        } else {
            mask[i] = 0;
            if (input_mask[i] & bad_pixel_bitmask) {
                mask[i] |= (1 << ErrorPixelBit);
            }
            // User and chip gap are just transferred
            if ((input_mask[i] & (1 << UserMaskedPixelBit)) != 0) {
                mask[i] |= (1 << UserMaskedPixelBit);
            }
            if ((input_mask[i] & (1 << ChipGapPixelBit)) != 0) {
                mask[i] |= (1 << ChipGapPixelBit);
            }
        }
    }
    raw_mask = {}; // For DECTRIS - there is no raw mask
    UpdateBinaryMask();
}

void PixelMask::LoadDarkBadPixelMask(const DiffractionExperiment& experiment, const std::vector<uint32_t> &input_mask) {
    if (input_mask.size() != mask.size())
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "Input match doesn't fit the detector ");

    for (int i = 0; i < mask.size(); i++) {
        // Ignore module gap (doesn't matter) or bad pixels
        if ((mask[i] & (1 << ModuleGapPixelBit | 1 << ErrorPixelBit)) != 0)
            continue;

        if (input_mask[i] != 0) {
            mask[i] |= (1 << NoisyPixelBit);
        } else {
            mask[i] &= ~(1 << NoisyPixelBit);
        }
    }
    UpdateDerived(experiment);
}