Jungfraujoch/process/JFJochProcessCommandLine.cpp

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

#include "JFJochProcessCommandLine.h"
#include "../common/DiffractionExperiment.h"

#include <sstream>
#include <vector>

namespace {
    std::string quote_if_needed(const std::string &s) {
        if (s.find_first_of(" \t\"'") == std::string::npos)
            return s;
        std::string out = "\"";
        for (char c: s) {
            if (c == '"' || c == '\\')
                out += '\\';
            out += c;
        }
        out += '"';
        return out;
    }

    const char *indexing_alg_flag(IndexingAlgorithmEnum a) {
        switch (a) {
            case IndexingAlgorithmEnum::FFBIDX: return "ffbidx";
            case IndexingAlgorithmEnum::FFT:    return "fft";
            case IndexingAlgorithmEnum::FFTW:   return "fftw";
            case IndexingAlgorithmEnum::None:   return "none";
            case IndexingAlgorithmEnum::Auto:
            default:                            return "auto";
        }
    }

    const char *refine_flag(GeomRefinementAlgorithmEnum r) {
        switch (r) {
            case GeomRefinementAlgorithmEnum::None:            return "none";
            case GeomRefinementAlgorithmEnum::OrientationOnly: return "orientation";
            case GeomRefinementAlgorithmEnum::BeamCenter:
            default:                                           return "beam_and_lattice";
        }
    }

    std::string num(double v) {
        std::ostringstream o;
        o << v;
        return o.str();
    }
}

std::string JFJochProcessCommandLine(const ProcessConfig &config,
                                     const DiffractionExperiment &experiment,
                                     const std::string &input_file) {
    std::vector<std::string> args;
    const bool azint = (config.mode == ProcessMode::AzimuthalIntegration);
    args.emplace_back(azint ? "jfjoch_azint" : "jfjoch_process");

    auto add = [&](const std::string &flag, const std::string &val) {
        args.push_back(flag);
        args.push_back(val);
    };

    if (!config.output_prefix.empty())
        add("-o", config.output_prefix);
    add("-N", std::to_string(config.nthreads));
    if (config.start_image != 0)
        add("-s", std::to_string(config.start_image));
    if (config.end_image >= 0)
        add("-e", std::to_string(config.end_image));
    if (config.stride != 1)
        add("-t", std::to_string(config.stride));

    if (azint) {
        const auto a = experiment.GetAzimuthalIntegrationSettings();
        add("--min-q", num(a.GetLowQ_recipA()));
        add("--max-q", num(a.GetHighQ_recipA()));
        add("--q-spacing", num(a.GetQSpacing_recipA()));
        add("--azimuthal-bins", std::to_string(a.GetAzimuthalBinCount()));
        add("--polarization-correction", a.IsPolarizationCorrection() ? "on" : "off");
        add("--solid-angle-correction", a.IsSolidAngleCorrection() ? "on" : "off");
    } else {
        const auto &sf = config.spot_finding;
        add("--spot-sigma", num(sf.signal_to_noise_threshold));
        add("--spot-threshold", std::to_string(sf.photon_count_threshold));
        add("--spot-high-resolution", num(sf.high_resolution_limit));
        add("--max-spots", std::to_string(experiment.GetMaxSpotCount()));

        const auto idx = experiment.GetIndexingSettings();
        add("-X", indexing_alg_flag(idx.GetAlgorithm()));
        add("-r", refine_flag(idx.GetGeomRefinementAlgorithm()));

        if (const auto sg = experiment.GetSpaceGroupNumber())
            add("-S", std::to_string(*sg));
        if (const auto uc = experiment.GetUnitCell()) {
            std::ostringstream o;
            o << uc->a << "," << uc->b << "," << uc->c << "," << uc->alpha << "," << uc->beta << "," << uc->gamma;
            add("-C", o.str());
        }
        if (const auto bw = experiment.GetBandwidthFWHM())
            add("--bandwidth", num(*bw));

        const auto bragg = experiment.GetBraggIntegrationSettings();
        std::ostringstream radii;
        radii << bragg.GetR1() << "," << bragg.GetR2() << "," << bragg.GetR3();
        add("--integration-radius", radii.str());

        if (config.rotation_indexing) {
            if (config.two_pass_rotation)
                add("-R", std::to_string(config.rotation_indexing_image_count));
            else
                args.emplace_back("--single-pass-rotation");
            if (!config.reuse_rotation_spots)
                args.emplace_back("--redo-rotation-spots");
        } else if (experiment.GetGoniometer().has_value()) {
            // rotation dataset processed as stills -> the user overrode the default with --force-still
            args.emplace_back("--force-still");
        }

        if (config.run_scaling) {
            args.emplace_back("-M");
            const auto sc = experiment.GetScalingSettings();
            if (!sc.GetMergeFriedel())
                args.emplace_back("-A");
            if (sc.GetRefineB())
                args.emplace_back("-B");
        }
    }

    args.push_back(input_file);

    std::ostringstream cmd;
    for (size_t i = 0; i < args.size(); i++) {
        if (i)
            cmd << ' ';
        cmd << quote_if_needed(args[i]);
    }
    return cmd.str();
}