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 <QFileDialog>
#include <QSignalBlocker>

#include <cmath>

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

JFJochViewerSettingsDock::JFJochViewerSettingsDock(const SpotFindingSettings &spot,
                                                   const IndexingSettings &indexing,
                                                   const AzimuthalIntegrationSettings &azint,
                                                   QWidget *parent)
    : QWidget(parent), spot_(spot), indexing_(indexing), azint_(azint) {

    // 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, stack, &QStackedWidget::setCurrentIndex);

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

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();
        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 *minPix = new SliderPlusBox(1.0, 20.0, 1.0, 0, page);
    minPix->setValue(std::lround(spot_.min_pix_per_spot));
    spot->addRow("Signal/noise", snr);
    spot->addRow("Photon count", count);
    spot->addRow("Min pixels/spot", minPix);
    spotSection->setContentLayout(spot);
    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 = static_cast<float>(v); EmitSpotFinding(); });
    connect(minPix, &SliderPlusBox::valueChanged, this, [this](double v) {
        spot_.min_pix_per_spot = std::lround(v); EmitSpotFinding(); });

    // --- Indexing ---
    auto *idxSection = new CollapsibleSection("Indexing", page);
    auto *idx = new QFormLayout();
    idx->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    auto *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())));
    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));
    refine->addItem("Pixel refinement", static_cast<int>(GeomRefinementAlgorithmEnum::PixelRefine));
    refine->setCurrentIndex(refine->findData(static_cast<int>(indexing_.GetGeomRefinementAlgorithm())));
    idx->addRow("Algorithm", algo);
    idx->addRow("Refinement", refine);
    idxSection->setContentLayout(idx);
    layout->addWidget(idxSection);
    connect(algo, &QComboBox::currentIndexChanged, this, [this, algo] {
        indexing_.Algorithm(static_cast<IndexingAlgorithmEnum>(algo->currentData().toInt()));
        EmitSpotFinding();
    });
    connect(refine, &QComboBox::currentIndexChanged, this, [this, refine] {
        indexing_.GeomRefinementAlgorithm(static_cast<GeomRefinementAlgorithmEnum>(refine->currentData().toInt()));
        EmitSpotFinding();
    });

    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, reference-based scaling and PixelRefine. 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);

    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);
    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);
    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::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();
}

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);
    }
}