Jungfraujoch/reader/NXmxModules.cpp

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

#include "NXmxModules.h"

#include <cmath>

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

namespace {

// A translation dataset as a vector in pixels of the internal frame (x = column, y = row, z = beam).
Coord ReadTranslation_px(HDF5Object &file, const std::string &path, double pixel_size_m, const RotMatrix &delta) {
    HDF5DataSet ds(file, path);
    std::vector<double> value;
    ds.ReadVector(value);
    const auto vec = ds.ReadAttrVec("vector");
    if (value.empty() || vec.size() != 3)
        throw JFJochException(JFJochExceptionCategory::HDF5, path + ": not a translation");
    double scale = 1.0;
    if (ds.AttrExists("units")) {
        const std::string units = ds.ReadAttrStr("units");
        if (units == "mm")
            scale = 1e-3;
        else if (units == "um" || units == "microns")
            scale = 1e-6;
    }
    const double len_px = value[0] * scale / pixel_size_m;
    // McStas -> internal is a half turn about z; the discrete image orientation is undone after it.
    const Coord mcstas(static_cast<float>(-vec[0]), static_cast<float>(-vec[1]), static_cast<float>(vec[2]));
    return delta.transpose() * (static_cast<float>(len_px) * mcstas);
}

}  // namespace

std::string NXmxModuleGroup(HDF5Object &file, size_t n) {
    // The index is written zero-padded to the width of the last one (module_00 ... module_15); the width is
    // the one module 0 has.
    for (size_t digits = 1; digits <= 3; digits++) {
        const std::string first = "/entry/instrument/detector/module_" + std::string(digits - 1, '0') + "0/";
        if (file.Exists(first + "data_origin")) {
            std::string index = std::to_string(n);
            if (index.size() < digits)
                index.insert(0, digits - index.size(), '0');
            const std::string base = "/entry/instrument/detector/module_" + index + "/";
            return file.Exists(base + "data_origin") ? base : "";
        }
    }
    return "";
}

DetectorModules ReadNXmxModules(HDF5Object &file, double pixel_size_m, const DetectorOrientation &orientation) {
    const RotMatrix delta = orientation.Matrix();
    std::vector<DetectorModule> out;
    for (size_t n = 0;; n++) {
        const std::string base = NXmxModuleGroup(file, n);
        if (base.empty())
            break;
        const auto origin = file.ReadVector<int64_t>(base + "data_origin");
        const auto size = file.ReadVector<int64_t>(base + "data_size");
        if (origin.size() != 2 || size.size() != 2)
            throw JFJochException(JFJochExceptionCategory::HDF5, base + ": only two-dimensional modules are read");
        const Coord o = ReadTranslation_px(file, base + "module_offset", pixel_size_m, delta);
        const Coord f = ReadTranslation_px(file, base + "fast_pixel_direction", pixel_size_m, delta);
        const Coord s = ReadTranslation_px(file, base + "slow_pixel_direction", pixel_size_m, delta);
        if (std::fabs(o.z) > 1e-3 || std::fabs(f.z) > 1e-6 || std::fabs(s.z) > 1e-6)
            throw JFJochException(JFJochExceptionCategory::HDF5, base + ": a module out of the detector plane is not read");
        DetectorModule m;
        m.y0 = origin[0];
        m.x0 = origin[1];
        m.height = size[0];
        m.width = size[1];
        m.ox = o.x;
        m.oy = o.y;
        m.fx = f.x;
        m.fy = f.y;
        m.sx = s.x;
        m.sy = s.y;
        // The readout axes, where the writer says (writer/NXmxModules.cpp); else the module's own array.
        if (file.Exists(base + "readout_fast_axis") && file.Exists(base + "readout_slow_axis")) {
            m.fast = DirectionFromName(file.GetString(base + "readout_fast_axis"));
            m.slow = DirectionFromName(file.GetString(base + "readout_slow_axis"));
        }
        out.push_back(m);
    }
    if (out.size() < 2)
        return {};
    return DetectorModules(out);
}