Jungfraujoch/viewer/widgets/JFJochViewerSettingsDock.cpp

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

#include "JFJochViewerSettingsDock.h"

#include <QVBoxLayout>
#include <QHBoxLayout>
#include <QFormLayout>
#include <QPushButton>
#include <QButtonGroup>
#include <QStackedWidget>
#include <QCheckBox>
#include <QComboBox>
#include <QLabel>
#include <QSignalBlocker>
#include <QFileDialog>
#include <QIcon>
#include <QPixmap>
#include <QPainter>

#include <cmath>

#include "SliderPlusBox.h"
#include "NumberLineEdit.h"
#include "PowderCalibrationWidget.h"
#include "CollapsibleSection.h"
#include "../../common/JFJochMath.h"
#include "../../common/CUDAWrapper.h"
#include "../../gemmi_gph/gemmi/symmetry.hpp"

namespace {
    // A single diffraction frame (image) vs a stack of frames (dataset), drawn white so they read on
    // the navy "Analyze" hero buttons.
    QIcon FramesIcon(int frames) {
        const int S = 28;
        QPixmap pm(S, S);
        pm.fill(Qt::transparent);
        QPainter p(&pm);
        p.setRenderHint(QPainter::Antialiasing);
        p.setPen(QPen(Qt::white, 2.0));
        p.setBrush(Qt::NoBrush);
        const double side = 13.0, step = 4.0;
        for (int i = frames - 1; i >= 0; --i)
            p.drawRoundedRect(QRectF(4 + i * step, 4 + i * step, side, side), 2.5, 2.5);
        p.setBrush(Qt::white);   // a diffraction "spot" in the front frame
        p.drawEllipse(QPointF(4 + side / 2.0, 4 + side / 2.0), 2.0, 2.0);
        p.end();
        return QIcon(pm);
    }
}

JFJochViewerSettingsDock::JFJochViewerSettingsDock(const SpotFindingSettings &spot,
                                                   const IndexingSettings &indexing,
                                                   const AzimuthalIntegrationSettings &azint,
                                                   const BraggIntegrationSettings &bragg,
                                                   const ScalingSettings &scaling,
                                                   QWidget *parent)
    : QWidget(parent), spot_(spot), indexing_(indexing), azint_(azint), bragg_(bragg), scaling_(scaling) {

    auto *layout = new QVBoxLayout(this);

    // The two analysis actions sit on top of the panel. "Analyze image" is a toggle (re-analyse the
    // current frame now and on every change while armed); "Analyze dataset" launches a processing job
    // whose kind (MX vs azimuthal) is decided by the MX/AzInt toggle below — no separate switch.
    const QString heroStyle =
        "QPushButton { background-color:#1F3A5F; color:white; border:none; border-radius:3px;"
        " padding:5px 10px; } QPushButton:hover { background-color:#16314f; }"
        " QPushButton:checked { background-color:#FA7268; } QPushButton:disabled { background-color:#9aa6b3; }";
    auto *analyzeImageBtn = new QPushButton(FramesIcon(1), " Analyze image", this);
    analyzeImageBtn->setCheckable(true);
    analyzeImageBtn->setStyleSheet(heroStyle);
    analyzeImageBtn->setToolTip("Re-analyse the current image now, and keep re-analysing on every"
                                " image / settings change while active");
    analyzeDatasetBtn_ = new QPushButton(FramesIcon(3), " Analyze dataset", this);
    analyzeDatasetBtn_->setStyleSheet(heroStyle);
    analyzeDatasetBtn_->setToolTip("Process the whole dataset (MX or azimuthal, per the toggle below)");
    auto *analyzeRow = new QHBoxLayout();
    analyzeRow->addWidget(analyzeImageBtn);
    analyzeRow->addWidget(analyzeDatasetBtn_);
    layout->addLayout(analyzeRow);
    layout->addSpacing(10);
    connect(analyzeImageBtn, &QPushButton::toggled, this, &JFJochViewerSettingsDock::reanalyzeImage);
    connect(analyzeDatasetBtn_, &QPushButton::clicked, this, [this] { emit analyzeDataset(azint_mode_); });

    // Segmented MX / AzInt toggle: the two communities pick their page; pages never share a screen.
    auto *mxButton = new QPushButton("MX", this);
    auto *azButton = new QPushButton("AzInt", this);
    for (auto *b : {mxButton, azButton}) {
        b->setCheckable(true);
        b->setStyleSheet("QPushButton:checked { background-color: #1F3A5F; color: white; }");
    }
    mxButton->setChecked(true);
    auto *group = new QButtonGroup(this);
    group->setExclusive(true);
    group->addButton(mxButton, 0);
    group->addButton(azButton, 1);

    auto *toggleRow = new QHBoxLayout();
    toggleRow->setSpacing(0);
    toggleRow->addWidget(mxButton);
    toggleRow->addWidget(azButton);

    auto *stack = new QStackedWidget(this);
    stack->addWidget(BuildMXPage());
    stack->addWidget(BuildAzIntPage());
    connect(group, &QButtonGroup::idClicked, this, [this, stack](int id) {
        azint_mode_ = (id == 1);
        stack->setCurrentIndex(id);
    });

    // Geometry is common to both communities, so it lives above the toggle rather than per page.
    layout->addLayout(toggleRow);
    layout->addWidget(BuildGeometrySection());
    layout->addWidget(stack);
    layout->addStretch();
}

void JFJochViewerSettingsDock::setHttpConnection(bool connected, QString) {
    analyzeDatasetBtn_->setEnabled(!connected);
    analyzeDatasetBtn_->setToolTip(connected
        ? "Dataset re-processing is only available for an open file, not a live HTTP stream"
        : "Process the whole dataset (MX or azimuthal, per the toggle below)");
}

QWidget *JFJochViewerSettingsDock::BuildGeometrySection() {
    auto *section = new CollapsibleSection("Geometry", this);
    auto *geom = new QFormLayout();
    geom->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);   // fields fill the panel width

    energy_ = new NumberLineEdit(1.0, 200.0, 12.4, 4, "keV", this);
    distance_ = new NumberLineEdit(10.0, 5000.0, 100.0, 2, "mm", this);
    beamX_ = new NumberLineEdit(-20000.0, 20000.0, 0.0, 1, "px", this);
    beamY_ = new NumberLineEdit(-20000.0, 20000.0, 0.0, 1, "px", this);
    rot1_ = new NumberLineEdit(-180.0, 180.0, 0.0, 3, "°", this);
    rot2_ = new NumberLineEdit(-180.0, 180.0, 0.0, 3, "°", this);

    // The detector origin is the PONI (PyFAI) point; in MX (XDS-style) terms it is the beam origin,
    // which coincides with the beam center only when the detector is untilted.
    const QString beamTip =
        "Beam origin (XDS convention): the PONI point where the un-tilted beam meets the detector. "
        "Equals the beam center only when the detector tilt is zero.";
    beamX_->setToolTip(beamTip);
    beamY_->setToolTip(beamTip);
    const QString tiltTip = "Detector tilt about the two in-plane axes (PyFAI PONI rot1 / rot2), in degrees.";
    rot1_->setToolTip(tiltTip);
    rot2_->setToolTip(tiltTip);

    auto *beam = new QHBoxLayout();
    beam->addWidget(beamX_);
    beam->addWidget(beamY_);
    auto *tilt = new QHBoxLayout();
    tilt->addWidget(rot1_);
    tilt->addWidget(rot2_);

    geom->addRow("Photon energy", energy_);
    geom->addRow("Detector distance", distance_);
    geom->addRow("Beam origin", beam);
    geom->addRow("Detector tilt", tilt);

    for (auto *f : {energy_, distance_, beamX_, beamY_, rot1_, rot2_})
        connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });

    section->setContentLayout(geom);
    return section;
}

QWidget *JFJochViewerSettingsDock::BuildMXPage() {
    auto *page = new QWidget(this);
    auto *layout = new QVBoxLayout(page);
    layout->setContentsMargins(0, 0, 0, 0);

    // --- Unit cell + space group (new: no input existed before) ---
    auto *cellSection = new CollapsibleSection("Unit cell", page);
    auto *cell = new QFormLayout();
    cell->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    cellKnown_ = new QCheckBox("Known unit cell", page);
    cell->addRow("", cellKnown_);
    cellA_ = new NumberLineEdit(1.0, 2000.0, 79.0, 3, "Å", page);
    cellB_ = new NumberLineEdit(1.0, 2000.0, 79.0, 3, "Å", page);
    cellC_ = new NumberLineEdit(1.0, 2000.0, 38.0, 3, "Å", page);
    cellAlpha_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", page);
    cellBeta_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", page);
    cellGamma_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", page);
    spaceGroup_ = new NumberLineEdit(0.0, 230.0, 0.0, 0, "", page);
    spaceGroup_->setToolTip("Space group number (1–230); 0 = unset.");
    spaceGroupName_ = new QLabel("—", page);
    auto *abc = new QHBoxLayout();
    abc->addWidget(cellA_); abc->addWidget(cellB_); abc->addWidget(cellC_);
    auto *angles = new QHBoxLayout();
    angles->addWidget(cellAlpha_); angles->addWidget(cellBeta_); angles->addWidget(cellGamma_);
    // Number and symbol split the line evenly, like the beam-origin row.
    auto *sgRow = new QHBoxLayout();
    sgRow->addWidget(spaceGroup_, 1);
    sgRow->addWidget(spaceGroupName_, 1);
    cell->addRow("a, b, c", abc);
    cell->addRow("α, β, γ", angles);
    cell->addRow("Space group", sgRow);
    cellSection->setContentLayout(cell);
    layout->addWidget(cellSection);

    auto enableCellFields = [this](bool on) {
        for (auto *f : {cellA_, cellB_, cellC_, cellAlpha_, cellBeta_, cellGamma_, spaceGroup_})
            f->setEnabled(on);
    };
    enableCellFields(false);
    connect(cellKnown_, &QCheckBox::toggled, this, [this, enableCellFields](bool on) {
        enableCellFields(on);
        UpdateSpaceGroupName();
        UpdateAlgorithmDescription();   // Auto resolves to FFBIDX vs FFT depending on a known cell
        EmitExperiment();
    });
    for (auto *f : {cellA_, cellB_, cellC_, cellAlpha_, cellBeta_, cellGamma_})
        connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });
    connect(spaceGroup_, &NumberLineEdit::newValue, this, [this] {
        UpdateSpaceGroupName();
        EmitExperiment();
    });

    // --- Spot finding ---
    auto *spotSection = new CollapsibleSection("Spot finding", page);
    auto *spot = new QFormLayout();
    spot->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    auto *snr = new SliderPlusBox(1.0, 10.0, 0.1, 1, page);
    snr->setValue(spot_.signal_to_noise_threshold);
    auto *count = new SliderPlusBox(0.0, 100.0, 1.0, 0, page);
    count->setValue(std::lround(spot_.photon_count_threshold));
    auto *highResSpot = new SliderPlusBox(0.5, 5.0, 0.1, 1, page);
    highResSpot->setValue(spot_.high_resolution_limit);
    auto *minPix = new NumberLineEdit(1.0f, 50.0f, static_cast<float>(spot_.min_pix_per_spot), 0, "px", page);
    auto *maxSpots = new NumberLineEdit(10.0f, 100000.0f, static_cast<float>(max_spots_), 0, "", page);
    spot->addRow("Signal/noise", snr);
    spot->addRow("Photon count", count);
    spot->addRow("High resolution [Å]", highResSpot);
    spot->addRow("Min pixels/spot", minPix);
    spot->addRow("Max spots/image", maxSpots);
    spotSection->setContentLayout(spot);
    spotSection->setExpanded(false);
    layout->addWidget(spotSection);
    connect(snr, &SliderPlusBox::valueChanged, this, [this](double v) {
        spot_.signal_to_noise_threshold = static_cast<float>(v); EmitSpotFinding(); });
    connect(count, &SliderPlusBox::valueChanged, this, [this](double v) {
        spot_.photon_count_threshold = std::llround(v); EmitSpotFinding(); });
    connect(highResSpot, &SliderPlusBox::valueChanged, this, [this](double v) {
        spot_.high_resolution_limit = static_cast<float>(v); EmitSpotFinding(); });
    connect(minPix, &NumberLineEdit::newValue, this, [this, minPix] {
        spot_.min_pix_per_spot = std::llround(minPix->value()); EmitSpotFinding(); });
    connect(maxSpots, &NumberLineEdit::newValue, this, [this, maxSpots] {
        max_spots_ = std::llround(maxSpots->value()); EmitSpotFinding(); });

    // --- Indexing ---
    auto *idxSection = new CollapsibleSection("Indexing", page);
    auto *idx = new QFormLayout();
    idx->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    algo_ = new QComboBox(page);
    algo_->addItem("Auto", static_cast<int>(IndexingAlgorithmEnum::Auto));
    algo_->addItem("FFBIDX (GPU, known cell)", static_cast<int>(IndexingAlgorithmEnum::FFBIDX));
    algo_->addItem("FFT (GPU, de-novo)", static_cast<int>(IndexingAlgorithmEnum::FFT));
    algo_->addItem("FFTW (CPU, de-novo)", static_cast<int>(IndexingAlgorithmEnum::FFTW));
    algo_->addItem("None", static_cast<int>(IndexingAlgorithmEnum::None));
    algo_->setCurrentIndex(algo_->findData(static_cast<int>(indexing_.GetAlgorithm())));
    algoDesc_ = new QLabel(page);
    algoDesc_->setWordWrap(true);
    algoDesc_->setStyleSheet("color: gray;");
    auto *refine = new QComboBox(page);
    refine->addItem("None", static_cast<int>(GeomRefinementAlgorithmEnum::None));
    refine->addItem("Orientation only", static_cast<int>(GeomRefinementAlgorithmEnum::OrientationOnly));
    refine->addItem("Beam center + lattice", static_cast<int>(GeomRefinementAlgorithmEnum::BeamCenter));
    // "Flex" (the CLI's -r flex): tries all per-image refinements and keeps whichever indexes the most
    // spots — lets the pipeline decide. Named "Flex", not "multi", to avoid the CrystFEL sense of multi
    // (multi-lattice integration).
    refine->addItem("Flex (best per-image refinement)", static_cast<int>(GeomRefinementAlgorithmEnum::Flex));
    refine->setCurrentIndex(refine->findData(static_cast<int>(indexing_.GetGeomRefinementAlgorithm())));
    // One high-level mode switch instead of separate partiality / rot3d / rotation-indexing options:
    // for a rotation dataset, unchecked = the rotation good-path (rotation indexing + Rotation
    // partiality + rot3d combine + scale-fulls), checked = treat it as stills (fixed partiality,
    // per-frame indexing). Disabled (and a no-op) for datasets that are already stills.
    stills_ = new QCheckBox("Process as stills", page);
    stills_->setEnabled(false);   // datasetLoaded enables it only for rotation (goniometer) datasets
    stills_->setToolTip("Treat a rotation dataset as independent stills (fixed partiality, per-frame "
                        "indexing). Unchecked on a rotation dataset = rotation indexing + 3D rotation scaling.");
    idx->addRow("Algorithm", algo_);
    idx->addRow("", algoDesc_);
    idx->addRow("Refinement", refine);
    idx->addRow("", stills_);
    idxSection->setContentLayout(idx);
    idxSection->setExpanded(false);
    layout->addWidget(idxSection);
    connect(algo_, &QComboBox::currentIndexChanged, this, [this] {
        indexing_.Algorithm(static_cast<IndexingAlgorithmEnum>(algo_->currentData().toInt()));
        UpdateAlgorithmDescription();
        EmitSpotFinding();
    });
    connect(refine, &QComboBox::currentIndexChanged, this, [this, refine] {
        indexing_.GeomRefinementAlgorithm(static_cast<GeomRefinementAlgorithmEnum>(refine->currentData().toInt()));
        EmitSpotFinding();
    });
    connect(stills_, &QCheckBox::toggled, this, [this] { ApplyProcessingMode(); });
    UpdateAlgorithmDescription();

    layout->addWidget(BuildBraggSection());
    layout->addWidget(BuildScalingSection());
    layout->addWidget(BuildReferenceSection());

    layout->addStretch();   // anchor sections to the top so expanding an accordion grows downward
    return page;
}

QWidget *JFJochViewerSettingsDock::BuildReferenceSection() {
    // A reference dataset for scaling: drives CCref and reference-based scaling. It is
    // independent of the loaded data (the worker keeps it across file switches); this just lets the
    // user pick the MTZ + column and shows what it contains and whether it matches the data.
    auto *section = new CollapsibleSection("Reference dataset", this);
    auto *form = new QFormLayout();
    form->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);

    refButton_ = new QPushButton("Choose MTZ…", this);
    refColumn_ = new QComboBox(this);
    refColumn_->setEnabled(false);
    refColumn_->setToolTip("Reference intensity / structure-factor column (F is squared to an intensity).");
    refSummary_ = new QLabel("No reference loaded", this);
    refSummary_->setWordWrap(true);
    refWarning_ = new QLabel(this);
    refWarning_->setWordWrap(true);
    refWarning_->setVisible(false);

    form->addRow(refButton_);
    form->addRow("Column", refColumn_);
    form->addRow(refSummary_);
    form->addRow(refWarning_);
    section->setContentLayout(form);
    section->setExpanded(false);   // folded on start (only geometry + unit cell start open)

    connect(refButton_, &QPushButton::clicked, this, [this] {
        const QString path = QFileDialog::getOpenFileName(this, "Reference MTZ", refPath_,
                                                          "MTZ files (*.mtz);;All files (*)");
        if (path.isEmpty())
            return;
        refPath_ = path;
        emit referenceSelected(path, QString());   // empty column -> let the worker auto-select
    });
    // activated (not currentIndexChanged) so re-populating the combo on load doesn't re-trigger.
    connect(refColumn_, &QComboBox::activated, this, [this] {
        if (!refPath_.isEmpty())
            emit referenceSelected(refPath_, refColumn_->currentText());
    });

    return section;
}

QWidget *JFJochViewerSettingsDock::BuildAzIntPage() {
    auto *page = new QWidget(this);
    auto *layout = new QVBoxLayout(page);
    layout->setContentsMargins(0, 0, 0, 0);

    auto *azSection = new CollapsibleSection("Azimuthal integration", page);
    auto *az = new QFormLayout();
    az->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    auto *lowQ = new SliderPlusBox(1e-5, 10.0, 0.001, 4, page);
    lowQ->setValue(azint_.GetLowQ_recipA());
    auto *highQ = new SliderPlusBox(2e-5, 10.0, 0.001, 4, page);
    highQ->setValue(azint_.GetHighQ_recipA());
    auto *spacing = new SliderPlusBox(1e-5, 1.0, 0.001, 5, page, SliderPlusBox::ScaleType::Logarithmic);
    spacing->setValue(azint_.GetQSpacing_recipA());
    auto *azimBins = new QComboBox(page);
    for (int b : {1, 2, 4, 8, 16, 32, 64, 128})
        azimBins->addItem(QString::number(b), b);
    azimBins->setCurrentIndex(azimBins->findData(azint_.GetAzimuthalBinCount()));
    az->addRow("Low Q [Å⁻¹]", lowQ);
    az->addRow("High Q [Å⁻¹]", highQ);
    az->addRow("Q spacing [Å⁻¹]", spacing);
    az->addRow("Azimuthal bins", azimBins);
    azSection->setContentLayout(az);
    azSection->setExpanded(false);
    layout->addWidget(azSection);

    auto emitAz = [=, this] {
        azint_.QRange_recipA(static_cast<float>(lowQ->value()), static_cast<float>(highQ->value()));
        azint_.QSpacing_recipA(static_cast<float>(spacing->value()));
        azint_.AzimuthalBinCount(azimBins->currentData().toInt());
        emit azintChanged(azint_);
    };
    connect(lowQ, &SliderPlusBox::valueChanged, this, [emitAz] { emitAz(); });
    connect(highQ, &SliderPlusBox::valueChanged, this, [emitAz] { emitAz(); });
    connect(spacing, &SliderPlusBox::valueChanged, this, [emitAz] { emitAz(); });
    connect(azimBins, &QComboBox::currentIndexChanged, this, [emitAz] { emitAz(); });

    // Powder calibration (calibrant rings + geometry refinement) - reuse the existing widget.
    auto *powderSection = new CollapsibleSection("Powder calibration", page);
    auto *powderLayout = new QVBoxLayout();
    powderLayout->setContentsMargins(0, 0, 0, 0);
    powder_ = new PowderCalibrationWidget(page);
    connect(powder_, &PowderCalibrationWidget::findBeamCenter, this, &JFJochViewerSettingsDock::findBeamCenter);
    connect(powder_, &PowderCalibrationWidget::ringsFromCalibration, this, &JFJochViewerSettingsDock::ringsFromCalibration);
    powderLayout->addWidget(powder_);
    powderSection->setContentLayout(powderLayout);
    powderSection->setExpanded(false);
    layout->addWidget(powderSection);

    layout->addStretch();   // anchor sections to the top so expanding an accordion grows downward
    return page;
}

void JFJochViewerSettingsDock::EmitSpotFinding() {
    emit spotFindingChanged(spot_, indexing_, max_spots_);
}

void JFJochViewerSettingsDock::UpdateAlgorithmDescription() {
    if (!algo_ || !algoDesc_)
        return;
    const auto a = static_cast<IndexingAlgorithmEnum>(algo_->currentData().toInt());
    const bool gpu = get_gpu_count() > 0;
    const bool cell_known = cellKnown_ && cellKnown_->isChecked();
    QString text;
    switch (a) {
        case IndexingAlgorithmEnum::FFBIDX:
            text = "GPU, needs a known cell — best for sparse serial stills"; break;
        case IndexingAlgorithmEnum::FFT:
            text = "GPU, de-novo — best for strong rotation data"; break;
        case IndexingAlgorithmEnum::FFTW:
            text = "CPU, de-novo — no GPU needed"; break;
        case IndexingAlgorithmEnum::Auto: {
            const IndexingAlgorithmEnum r = !gpu ? IndexingAlgorithmEnum::FFTW
                : (cell_known ? IndexingAlgorithmEnum::FFBIDX : IndexingAlgorithmEnum::FFT);
            const QString rn = r == IndexingAlgorithmEnum::FFBIDX ? "FFBIDX"
                : r == IndexingAlgorithmEnum::FFT ? "FFT" : "FFTW";
            text = QString("resolves to %1 here (%2, cell %3)")
                       .arg(rn, gpu ? "GPU" : "no GPU", cell_known ? "known" : "unknown");
            break;
        }
        default:
            text = "no indexing"; break;
    }
    algoDesc_->setText(text);
}

QWidget *JFJochViewerSettingsDock::BuildBraggSection() {
    auto *section = new CollapsibleSection("Bragg integration", this);
    auto *form = new QFormLayout();
    form->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);

    auto *gaussian = new QCheckBox("Gaussian profile fit", this);
    gaussian->setChecked(bragg_.GetIntegrator() != IntegratorMode::BoxSum);
    gaussian->setToolTip("Profile-fit the spots (more accurate intensities); off = classical box-sum.");
    auto *r1 = new NumberLineEdit(1.0f, 30.0f, bragg_.GetR1(), 1, "px", this);
    auto *r2 = new NumberLineEdit(1.0f, 30.0f, bragg_.GetR2(), 1, "px", this);
    auto *r3 = new NumberLineEdit(1.0f, 30.0f, bragg_.GetR3(), 1, "px", this);
    auto *radii = new QHBoxLayout();
    radii->addWidget(r1); radii->addWidget(r2); radii->addWidget(r3);
    auto *stillPartiality = new QCheckBox("Stills partiality (experimental)", this);
    stillPartiality->setChecked(bragg_.GetStillPartiality());
    stillPartiality->setToolTip("Experimental, stills only: weight each reflection by a Gaussian "
                                "excitation-error partiality exp(-d_ewald²/2σ²) instead of treating it as a "
                                "full. Pairs with \"Partiality uncertainty\" in Scaling.");
    // Background trim: replace the r2..r3 ring mean with a symmetric trimmed mean (drop the lowest and
    // highest fraction of ring pixels), which removes the high-side bias that over-subtracts weak
    // high-angle reflections. Checkbox + fraction; 0 = plain mean.
    const float trim = bragg_.GetBackgroundTrimFraction();
    auto *bkgTrim = new QCheckBox("Background trim", this);
    bkgTrim->setChecked(trim > 0.0f);
    bkgTrim->setToolTip("Estimate the local Bragg background with a symmetric trimmed mean of the "
                        "background ring (drop the lowest and highest fraction of pixels) instead of the "
                        "plain mean, removing the high-side bias that over-subtracts weak high-angle "
                        "reflections. 0.10 recommended; unchecked = plain mean.");
    auto *bkgTrimFrac = new NumberLineEdit(0.01f, 0.49f, trim > 0.0f ? trim : 0.10f, 2, "", this);
    bkgTrimFrac->setEnabled(bkgTrim->isChecked());
    auto *trimRow = new QHBoxLayout();
    trimRow->addWidget(bkgTrim);
    trimRow->addWidget(bkgTrimFrac, 1);
    form->addRow("", gaussian);
    form->addRow("Radii r1/r2/r3", radii);
    form->addRow("", stillPartiality);
    form->addRow("", trimRow);
    section->setContentLayout(form);
    section->setExpanded(false);   // folded on start (only geometry + unit cell start open)

    auto emitBragg = [=, this] {
        bragg_.Integrator(gaussian->isChecked() ? IntegratorMode::ProfileGaussian : IntegratorMode::BoxSum);
        bragg_.R1(static_cast<float>(r1->value())).R2(static_cast<float>(r2->value()))
              .R3(static_cast<float>(r3->value()));
        bragg_.StillPartiality(stillPartiality->isChecked());
        bragg_.BackgroundTrimFraction(bkgTrim->isChecked() ? static_cast<float>(bkgTrimFrac->value()) : 0.0f);
        emit braggChanged(bragg_);
    };
    connect(gaussian, &QCheckBox::toggled, this, [emitBragg] { emitBragg(); });
    connect(stillPartiality, &QCheckBox::toggled, this, [emitBragg] { emitBragg(); });
    connect(bkgTrim, &QCheckBox::toggled, this,
            [bkgTrim, bkgTrimFrac, emitBragg] { bkgTrimFrac->setEnabled(bkgTrim->isChecked()); emitBragg(); });
    connect(bkgTrimFrac, &NumberLineEdit::newValue, this, [emitBragg] { emitBragg(); });
    for (auto *f : {r1, r2, r3})
        connect(f, &NumberLineEdit::newValue, this, [emitBragg] { emitBragg(); });
    return section;
}

QWidget *JFJochViewerSettingsDock::BuildScalingSection() {
    // The partiality model + rot3d combine + scale-fulls are driven by "Process as stills" (indexing
    // section); the panel keeps the full scaling_ so those fields are preserved here, not reset.
    auto *section = new CollapsibleSection("Scaling", this);
    auto *form = new QFormLayout();
    form->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);

    auto *friedel = new QCheckBox("Merge Friedel pairs", this);
    friedel->setChecked(scaling_.GetMergeFriedel());
    auto *refineB = new QCheckBox("Refine B-factor", this);
    refineB->setChecked(scaling_.GetRefineB());
    auto *corrections = new QCheckBox("Correction surfaces (decay + absorption)", this);
    corrections->setChecked(scaling_.GetCorrectionSurfaces());
    corrections->setToolTip("Rotation only: fit a radiation-damage decay and a goniometer-frame absorption "
                            "surface on the fulls. Cross-validated, so they no-op when their systematic is "
                            "absent. On by default.");
    auto *modulation = new QCheckBox("Detector-plane modulation (stills)", this);
    modulation->setChecked(scaling_.GetStillsModulation());
    modulation->setToolTip("Stills: fit a detector-plane modulation (flat-field) surface over where each "
                           "reflection lands, cross-validated so it no-ops when the systematic is absent. "
                           "For rotation, modulation is part of \"Correction surfaces\" above.");
    auto *limitRes = new QCheckBox("High-resolution limit", this);
    limitRes->setChecked(scaling_.GetHighResolutionLimit_A().has_value());
    auto *highRes = new NumberLineEdit(0.3f, 5.0f, scaling_.GetHighResolutionLimit_A().value_or(2.0), 1, "Å", this);
    highRes->setEnabled(limitRes->isChecked());

    // Stills partiality-uncertainty merge term: adds a systematic sigma ~c*(1-partiality)*<I> on partials,
    // so strong low-partiality partials are not over-trusted. Pairs with "Stills partiality" (Bragg); the
    // library auto-gates it to strong/medium data. 0 = off; ~2.5 recommended.
    const double part_unc = scaling_.GetPartialityUncertaintyCoeff();
    auto *partUncertain = new QCheckBox("Partiality uncertainty", this);
    partUncertain->setChecked(part_unc > 0.0);
    partUncertain->setToolTip("Stills: add a systematic merge σ ~c·(1−partiality)·⟨I⟩ to partials so strong "
                              "low-partiality partials are not over-trusted. Use with \"Stills partiality\"; "
                              "auto-gated to strong/medium data. ~2.5 recommended; unchecked = off.");
    auto *partUncertainCoeff = new NumberLineEdit(0.1f, 10.0f, part_unc > 0.0 ? part_unc : 2.5, 1, "", this);
    partUncertainCoeff->setEnabled(partUncertain->isChecked());

    form->addRow("", friedel);
    form->addRow("", refineB);
    form->addRow("", corrections);
    form->addRow("", modulation);
    // Compact, and aligned with the checkboxes above: the limit checkbox + value sit together in the
    // field column (not as a row label, which would indent it differently).
    auto *resRow = new QHBoxLayout();
    resRow->addWidget(limitRes);
    resRow->addWidget(highRes, 1);
    form->addRow("", resRow);
    auto *puRow = new QHBoxLayout();
    puRow->addWidget(partUncertain);
    puRow->addWidget(partUncertainCoeff, 1);
    form->addRow("", puRow);
    section->setContentLayout(form);
    section->setExpanded(false);   // folded on start (only geometry + unit cell start open)

    auto emitScaling = [=, this] {
        scaling_.MergeFriedel(friedel->isChecked());
        scaling_.RefineB(refineB->isChecked());
        scaling_.CorrectionSurfaces(corrections->isChecked());
        scaling_.StillsModulation(modulation->isChecked());
        scaling_.HighResolutionLimit_A(limitRes->isChecked()
            ? std::optional<double>(highRes->value()) : std::nullopt);
        scaling_.PartialityUncertaintyCoeff(partUncertain->isChecked() ? partUncertainCoeff->value() : 0.0);
        emit scalingChanged(scaling_);
    };
    connect(friedel, &QCheckBox::toggled, this, [emitScaling] { emitScaling(); });
    connect(refineB, &QCheckBox::toggled, this, [emitScaling] { emitScaling(); });
    connect(corrections, &QCheckBox::toggled, this, [emitScaling] { emitScaling(); });
    connect(modulation, &QCheckBox::toggled, this, [emitScaling] { emitScaling(); });
    connect(limitRes, &QCheckBox::toggled, this, [emitScaling, highRes](bool on) {
        highRes->setEnabled(on); emitScaling(); });
    connect(highRes, &NumberLineEdit::newValue, this, [emitScaling] { emitScaling(); });
    connect(partUncertain, &QCheckBox::toggled, this, [emitScaling, partUncertainCoeff](bool on) {
        partUncertainCoeff->setEnabled(on); emitScaling(); });
    connect(partUncertainCoeff, &NumberLineEdit::newValue, this, [emitScaling] { emitScaling(); });
    return section;
}

void JFJochViewerSettingsDock::EmitExperiment() {
    if (!have_experiment_)
        return;
    experiment_.IncidentEnergy_keV(static_cast<float>(energy_->value()));
    experiment_.DetectorDistance_mm(static_cast<float>(distance_->value()));
    experiment_.BeamX_pxl(static_cast<float>(beamX_->value()));
    experiment_.BeamY_pxl(static_cast<float>(beamY_->value()));
    experiment_.PoniRot1_rad(static_cast<float>(rot1_->value() * PI / 180.0));
    experiment_.PoniRot2_rad(static_cast<float>(rot2_->value() * PI / 180.0));
    if (cellKnown_->isChecked()) {
        experiment_.SetUnitCell(UnitCell{
            static_cast<float>(cellA_->value()), static_cast<float>(cellB_->value()),
            static_cast<float>(cellC_->value()), static_cast<float>(cellAlpha_->value()),
            static_cast<float>(cellBeta_->value()), static_cast<float>(cellGamma_->value())});
        const int sg = static_cast<int>(std::lround(spaceGroup_->value()));
        experiment_.SpaceGroupNumber(sg > 0 ? std::optional<int64_t>(sg) : std::nullopt);
    } else {
        experiment_.SetUnitCell(std::nullopt);
        experiment_.SpaceGroupNumber(std::nullopt);
    }
    emit experimentChanged(experiment_);
}

void JFJochViewerSettingsDock::RefreshGeometryFields() {
    // Populate fields from the loaded experiment. NumberLineEdit::setValue does not emit newValue
    // (that fires only on user editing), so this cannot feed back into EmitExperiment.
    energy_->setValue(experiment_.GetIncidentEnergy_keV());
    distance_->setValue(experiment_.GetDetectorDistance_mm());
    beamX_->setValue(experiment_.GetBeamX_pxl());
    beamY_->setValue(experiment_.GetBeamY_pxl());
    rot1_->setValue(experiment_.GetPoniRot1_rad() * 180.0 / PI);
    rot2_->setValue(experiment_.GetPoniRot2_rad() * 180.0 / PI);

    const auto cell = experiment_.GetUnitCell();
    QSignalBlocker blockKnown(cellKnown_);
    cellKnown_->setChecked(cell.has_value());
    for (auto *f : {cellA_, cellB_, cellC_, cellAlpha_, cellBeta_, cellGamma_, spaceGroup_})
        f->setEnabled(cell.has_value());
    if (cell) {
        cellA_->setValue(cell->a);   cellB_->setValue(cell->b);   cellC_->setValue(cell->c);
        cellAlpha_->setValue(cell->alpha); cellBeta_->setValue(cell->beta); cellGamma_->setValue(cell->gamma);
        spaceGroup_->setValue(experiment_.GetSpaceGroupNumber().value_or(0));
    }
    UpdateSpaceGroupName();
}

void JFJochViewerSettingsDock::UpdateSpaceGroupName() {
    if (!cellKnown_->isChecked()) {
        spaceGroupName_->setText("—");
        return;
    }
    const int n = static_cast<int>(std::lround(spaceGroup_->value()));
    if (n >= 1 && n <= 230) {
        try {
            const auto &sg = gemmi::get_spacegroup_by_number(n);   // Hermann–Mauguin short symbol
            spaceGroupName_->setText(QString::fromStdString(sg.short_name()));
        } catch (...) {
            spaceGroupName_->setText("invalid");
        }
    } else {
        spaceGroupName_->setText(n == 0 ? "—" : "invalid");
    }
}

void JFJochViewerSettingsDock::datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset) {
    if (!dataset)
        return;
    experiment_ = dataset->experiment;
    have_experiment_ = true;
    RefreshGeometryFields();

    // "Process as stills" only applies to a rotation dataset; enable it accordingly and apply the
    // resulting indexing/scaling mode so it reaches the worker.
    if (stills_) {
        stills_->setEnabled(experiment_.GetGoniometer().has_value());
        ApplyProcessingMode();
    }
}

void JFJochViewerSettingsDock::ApplyProcessingMode() {
    // Rotation good-path unless the dataset is stills or the user forces "Process as stills".
    const bool rotation_data = experiment_.GetGoniometer().has_value();
    const bool rotation_mode = rotation_data && stills_ && !stills_->isChecked();
    indexing_.RotationIndexing(rotation_mode);   // rotation indexing -> rotation scaling/merge downstream
    scaling_.ScaleFulls(rotation_mode);
    EmitSpotFinding();              // carries indexing_ (incl. RotationIndexing) to the worker
    emit scalingChanged(scaling_);
}

void JFJochViewerSettingsDock::loadImage(std::shared_ptr<const JFJochReaderImage> image) {
    if (powder_)
        powder_->loadImage(image);
}

void JFJochViewerSettingsDock::referenceLoaded(ReferenceMtzInfo info) {
    {
        QSignalBlocker block(refColumn_);   // re-populating must not emit referenceSelected
        refColumn_->clear();
        refColumn_->addItems(info.columns);
        const int idx = refColumn_->findText(info.used_column);
        if (idx >= 0)
            refColumn_->setCurrentIndex(idx);
    }
    refColumn_->setEnabled(info.loaded && !info.columns.isEmpty());
    refSummary_->setText(info.loaded ? info.summary : "No reference loaded");

    if (info.warning.isEmpty()) {
        refWarning_->setVisible(false);
    } else {
        // Amber = a loaded-but-mismatched reference (a caution); red = a load failure.
        refWarning_->setStyleSheet(info.loaded ? "color: #B8860B;" : "color: #C0392B;");
        refWarning_->setText(info.warning);
        refWarning_->setVisible(true);
    }
}