Jungfraujoch/rugnux/RugnuxCommandLine.cpp

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

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

#include <cmath>
#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::Flex:            return "flex";
            case GeomRefinementAlgorithmEnum::BeamCenter:
            default:                                           return "beam_and_lattice";
        }
    }

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

std::string RugnuxCommandLine(const ProcessConfig &config,
                                     const DiffractionExperiment &experiment,
                                     const std::string &input_file,
                                     const std::string &calibrant_name) {
    std::vector<std::string> args;
    const bool azint = (config.mode == ProcessMode::AzimuthalIntegration);
    const bool calibration = (config.mode == ProcessMode::Calibration);
    args.emplace_back("rugnux");
    if (azint) {
        args.emplace_back("--mode");
        args.emplace_back("azint");
    } else if (calibration) {
        args.emplace_back("--mode");
        args.emplace_back("calibration");
    }

    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));
    // Beam-stop detection is ON by default in the CLI, so emit only a deviation from that. getopt takes
    // an optional argument only when attached (=N), never as a separate token.
    if (!config.detect_beam_stop.has_value())
        args.emplace_back("--detect-beam-stop=off");
    else if (*config.detect_beam_stop != 60)
        args.push_back("--detect-beam-stop=" + std::to_string(*config.detect_beam_stop));
    // Measuring the beam centre is OFF by default in the CLI, and the flag fits the spindle with it.
    if (config.estimate_beam_center) {
        args.emplace_back("--estimate-beam-center");
        if (!config.fit_spindle)
            args.emplace_back("--no-fit-spindle");
    }

    if (calibration) {
        if (!calibrant_name.empty())
            add("--calibrant", calibrant_name);
        add("--calibration", config.calibration_method == CalibrationMethod::Rings ? "rings" : "spots");
        if (!config.calibration_refine_tilt)
            args.emplace_back("--no-refine-tilt");
        // The rings method reads the ring at every azimuth, and the GUI may have raised the sector
        // count for this run, so emit the value actually used rather than relying on the CLI default.
        if (config.calibration_method == CalibrationMethod::Rings)
            add("--azim-phi-bins",
                std::to_string(experiment.GetAzimuthalIntegrationSettings().GetAzimuthalBinCount()));
    } else if (azint) {
        const auto a = experiment.GetAzimuthalIntegrationSettings();
        add("--azim-min-q", num(a.GetLowQ_recipA()));
        // An unset maximum Q means "to the detector edge"; emitting the resolved number would pin it
        // to this run's geometry, so leave the flag out and let it resolve again.
        if (const auto high_q = a.GetRequestedHighQ_recipA())
            add("--azim-max-q", num(*high_q));
        add("--azim-q-spacing", num(a.GetQSpacing_recipA()));
        add("--azim-phi-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));
        // Emit the explicit flag rather than relying on the default, so the command line reproduces
        // this run even if the default changes.
        args.emplace_back(sf.adaptive_threshold ? "--adaptive-spots" : "--no-adaptive-spots");
        if (sf.adaptive_threshold)
            add("--spot-false-pixels", num(sf.false_pixels_per_frame));
        // min-pix is chosen per image unless an explicit value is given, so emit --min-pix-per-spot only
        // when a fixed min-pix was selected; its absence selects the adaptive per-image path.
        if (sf.min_pix_per_spot.has_value())
            add("--min-pix-per-spot", std::to_string(*sf.min_pix_per_spot));
        // Same for the spot-finding limit: absent means "as far as the detector reaches".
        if (sf.high_resolution_limit.has_value())
            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 (bragg.GetStencilKSigma() > 0.0f)
            add("--integration-stencil", num(bragg.GetStencilKSigma()));
        // Background ring: the CLI defaults to the 4 sigma high-side clip, so emit a flag only when the
        // GUI chose otherwise. The trim is the alternative estimator (it clears the clip), and a clip of
        // 0 with no trim is the plain ring mean, which needs the flag to be reproduced.
        if (bragg.GetBackgroundTrimFraction() > 0.0f)
            add("--background-trim", num(bragg.GetBackgroundTrimFraction()));
        else if (bragg.GetBackgroundClipNSigma() != BraggIntegrationSettings().GetBackgroundClipNSigma())
            add("--background-clip", num(bragg.GetBackgroundClipNSigma()));
        // Air by default, so emit the flag only for the other media - which nothing in the file can
        // state, and which therefore has to travel with the command line to reproduce the run.
        if (bragg.GetFlightPath() == FlightPathMedium::Helium)
            add("--flight-path", "helium");
        else if (bragg.GetFlightPath() == FlightPathMedium::Vacuum)
            add("--flight-path", "vacuum");
        if (const auto max_hkl = bragg.GetMaxHKL())
            add("--max-hkl", std::to_string(*max_hkl));
        // Unset means "to the detector edge"; emitting the resolved number would pin it to this run's
        // geometry, so leave the flag out and let it resolve again.
        if (const auto d_min = bragg.GetDMinLimit_A())
            add("--integration-high-resolution", num(*d_min));

        if (config.rotation_indexing) {
            if (config.two_pass_rotation)
                // -R takes an optional argument, which getopt only accepts attached (-R100), never as a
                // separate token - so emit it joined or the copied command line will not re-parse.
                args.push_back("-R" + std::to_string(config.rotation_indexing_image_count));
            else
                args.emplace_back("--single-pass-rotation");
        } else if (experiment.GetGoniometer().has_value()) {
            // rotation dataset processed as stills -> the user overrode the default with --force-still
            args.emplace_back("--force-still");
        }

        // Stills geometry-refinement two-pass (--refine-geometry). getopt takes its optional argument
        // only when attached (=N), never as a separate token, so emit it joined. The CLI defaults it ON
        // for a stills-with-cell run, so emit =off when the GUI turned it off in that same case, to
        // reproduce the GUI's choice in the copied command line.
        const bool stills_with_cell = !config.rotation_indexing && experiment.GetUnitCell().has_value();
        if (config.refine_geometry.has_value())
            args.push_back("--refine-geometry=" + std::to_string(*config.refine_geometry));
        else if (stills_with_cell)
            args.emplace_back("--refine-geometry=off");

        // Rotation two-pass geometry post-refine. The CLI defaults it ON for a rotation run, so emit the
        // disable flag only when the GUI turned it off on a rotation dataset (to reproduce that choice).
        if (config.rotation_indexing && !config.rotation_postrefine_geometry)
            args.emplace_back("--rotation-no-postrefine");
        if (config.rotation_scale.has_value())
            add("--rotation-scale", num(*config.rotation_scale));

        // Merging is on by default; emit --no-merge only when it was turned off.
        if (config.run_scaling) {
            const auto sc = experiment.GetScalingSettings();
            if (!sc.GetMergeFriedel())
                args.emplace_back("-A");
            if (!sc.GetStillsPartialityRefine())
                args.emplace_back("--simple-stills");
            if (!sc.GetExpectedVarianceMerge())
                args.emplace_back("--no-expected-variance-merge");
            // When merging, the CLI skips the large _process.h5 unless asked; emit the flag when it is
            // wanted so a copied command matches the GUI's "Save _process.h5" choice. (write_merged has
            // no CLI equivalent - the CLI always writes the .mtz/.cif when merging.)
            if (config.write_process_h5)
                args.emplace_back("--write-process-h5");
            // The low-resolution limit is on by default at the same value in both, so emit it only when
            // it differs - including 0, which is how the CLI spells "no limit".
            const auto d_max = sc.GetLowResolutionLimit_A();
            const auto d_max_default = ScalingSettings().GetLowResolutionLimit_A();
            if (d_max != d_max_default)
                args.push_back("--scaling-low-resolution=" + num(d_max.value_or(0.0)));
            // An infinite d_max is the default of a run with no low limit, so d_min alone restates it.
            if (const auto r = sc.GetReportResolutionRange_A())
                args.push_back("--report-resolution=" + num(r->d_min)
                               + (std::isfinite(r->d_max) ? "," + num(r->d_max) : ""));
        } else {
            args.emplace_back("--no-merge");
        }
    }

    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();
}