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 <QRadioButton>
#include <QLabel>
#include <QLineEdit>
#include <QSignalBlocker>
#include <QFileDialog>
#include <QIcon>
#include <QPixmap>
#include <QPainter>

#include <cmath>

#include "../../common/Definitions.h"   // MAX_SPOT_COUNT
#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 {
    // What the goniometer fields offer when the file describes no sample motion, so picking a mode
    // on a still file starts from something sensible: the usual single rotation axis, and a raster
    // of the size beamlines commonly use.
    const char *DEFAULT_AXIS_NAME = "omega";
    constexpr float DEFAULT_AXIS[3] = {-1.0f, 0.0f, 0.0f};
    constexpr float DEFAULT_INCREMENT_DEG = 0.1f;
    constexpr float DEFAULT_GRID_N_FAST = 10.0f;
    constexpr float DEFAULT_GRID_STEP_UM = 20.0f;
    // Polarized fraction of a synchrotron beam - the same default a bare `rugnux` run applies.
    constexpr float DEFAULT_POLARIZATION = 0.99f;

    // 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),
      adaptive_min_pix_(!spot.min_pix_per_spot.has_value()),
      min_pix_value_(spot.min_pix_per_spot.value_or(2)) {

    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, azimuthal, calibration or grid scan, 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(mode_, powder_->Selection()); });

    // Segmented MX / AzInt / Calib / Grid toggle: each community picks its page; pages never share a
    // screen. The page is also the mode "Analyze dataset" runs, so there is one control, not two.
    auto *mxButton = new QPushButton("MX", this);
    auto *azButton = new QPushButton("AzInt", this);
    auto *calibButton = new QPushButton("Calib", this);
    auto *gridButton = new QPushButton("Grid", this);
    gridButton->setToolTip("Grid scan: score every cell of a raster and find the crystals in it. "
                           "Needs a dataset collected as a grid scan.");
    for (auto *b : {mxButton, azButton, calibButton, gridButton}) {
        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);
    group->addButton(calibButton, 2);
    group->addButton(gridButton, 3);

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

    auto *stack = new QStackedWidget(this);
    stack->addWidget(BuildMXPage());
    stack->addWidget(new QWidget(stack));   // AzInt: the shared section below is the whole page
    stack->addWidget(BuildCalibrationPage());
    stack->addWidget(BuildGridPage());
    connect(group, &QButtonGroup::idClicked, this, [this, stack](int id) {
        mode_ = id == 1 ? AnalysisMode::Azint
                        : id == 2 ? AnalysisMode::PowderCalibration
                        : id == 3 ? AnalysisMode::Grid : AnalysisMode::MXStills;
        stack->setCurrentIndex(id);
        // MX and Grid are the two crystal modes and share the four sections below; AzInt and Calib
        // need none of them.
        const bool crystal = (id == 0 || id == 3);
        for (auto *w : {cellSection_, goniometerSection_, spotFindingSection_, indexingSection_})
            w->setVisible(crystal);
        azintSection_->setVisible(id != 0);
    });

    // Geometry is common to all four, so it lives above the toggle rather than per page. Azimuthal
    // integration is common to three of them - a calibration by rings integrates the run in azimuthal
    // sectors and a grid scan's ice score reads the radial profile, and all of them need the same Q
    // range and spacing - so it is shared the same way and hidden only on MX.
    //
    // The crystal, goniometer, spot-finding and indexing sections are shared between MX and Grid for
    // the same reason: a raster is spot-found and (by default) indexed exactly as a still is, and the
    // goniometer section is also where the grid geometry itself is stated. They are built once and
    // shown per mode - a Grid copy of any of them would be a second control for one setting.
    layout->addLayout(toggleRow);
    layout->addWidget(BuildGeometrySection());
    cellSection_ = BuildUnitCellSection();
    goniometerSection_ = BuildGoniometerSection();
    spotFindingSection_ = BuildSpotFindingSection();
    indexingSection_ = BuildIndexingSection();
    for (auto *w : {cellSection_, goniometerSection_, spotFindingSection_, indexingSection_})
        layout->addWidget(w);
    azintSection_ = BuildAzIntSection();
    azintSection_->setVisible(false);   // MX is the page selected on start
    layout->addWidget(azintSection_);
    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, azimuthal, calibration or grid scan, 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);
    // Both are overwritten from the experiment as soon as a dataset is open; this is what they show
    // until then.
    polarizationOn_ = new QCheckBox("Polarization correction", this);
    polarizationOn_->setChecked(true);
    polarization_ = new NumberLineEdit(-1.0, 1.0, DEFAULT_POLARIZATION, 3, "", this);
    const QString polarizationTip =
        "Polarized fraction of the beam in the horizontal plane (XDS FRACTION_OF_POLARIZATION): 0.99 "
        "for a synchrotron, 0 for an unpolarized source. Divides out the Lp modulation in both the "
        "azimuthal profile and the integrated Bragg intensities; unchecked = no correction at all.";
    polarizationOn_->setToolTip(polarizationTip);
    polarization_->setToolTip(polarizationTip);

    // 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_);
    auto *polarization = new QHBoxLayout();
    polarization->addWidget(polarizationOn_);
    polarization->addWidget(polarization_, 1);

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

    for (auto *f : {energy_, distance_, beamX_, beamY_, rot1_, rot2_, polarization_})
        connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });
    connect(polarizationOn_, &QCheckBox::toggled, this, [this](bool on) {
        polarization_->setEnabled(on);
        EmitExperiment();
    });

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

QWidget *JFJochViewerSettingsDock::BuildUnitCellSection() {
    // Shared with the Grid page rather than kept on the MX one: a fixed-target raster is normally run
    // against a known cell, and that cell is what every raster cell is indexed with. The panel is the
    // only place the cell and space group can be stated, so hiding it on Grid would make the one
    // setting a serial experiment cares most about unreachable in the mode it is used in.
    auto *cellSection = new CollapsibleSection("Unit cell", this);
    auto *cell = new QFormLayout();
    cell->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    cellKnown_ = new QCheckBox("Known unit cell", this);
    cell->addRow("", cellKnown_);
    cellA_ = new NumberLineEdit(1.0, 2000.0, 79.0, 3, "Å", this);
    cellB_ = new NumberLineEdit(1.0, 2000.0, 79.0, 3, "Å", this);
    cellC_ = new NumberLineEdit(1.0, 2000.0, 38.0, 3, "Å", this);
    cellAlpha_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", this);
    cellBeta_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", this);
    cellGamma_ = new NumberLineEdit(1.0, 179.0, 90.0, 2, "°", this);
    spaceGroup_ = new NumberLineEdit(0.0, 230.0, 0.0, 0, "", this);
    spaceGroup_->setToolTip("Space group number (1–230); 0 = unset.");
    spaceGroupName_ = new QLabel("—", this);
    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);

    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();
    });

    return cellSection;
}

QWidget *JFJochViewerSettingsDock::BuildSpotFindingSection() {
    // Shared with the Grid page: a raster is scored out of the spots - the per-cell protein score and
    // the per-cell resolution both come from the spot finder, and the Grid job turns spot finding on
    // unconditionally - so these are the settings a Grid run is actually made of.
    auto *spotSection = new CollapsibleSection("Spot finding", this);
    auto *spot = new QFormLayout();
    spot->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    auto *snr = new SliderPlusBox(1.0, 10.0, 0.1, 1, this);
    snr->setValue(spot_.signal_to_noise_threshold);
    auto *count = new SliderPlusBox(0.0, 100.0, 1.0, 0, this);
    count->setValue(std::lround(spot_.photon_count_threshold));
    auto *adaptive = new QCheckBox("Adaptive threshold (per-ring, auto)", this);
    adaptive->setChecked(spot_.adaptive_threshold);
    adaptive->setToolTip("Self-calibrating detection: the strong-pixel threshold is derived from each "
                         "image's own per-resolution-ring noise, so one setting adapts across datasets. "
                         "The signal/noise and photon-count settings are not used while this is on. "
                         "Default for stills and rotation alike, as in rugnux.");
    auto *highResSpot = new SliderPlusBox(0.5, 5.0, 0.1, 1, this);
    highResSpot->setValue(spot_.high_resolution_limit.value_or(1.5f));
    auto *autoHighResSpot = new QCheckBox("To detector edge", this);
    autoHighResSpot->setChecked(!spot_.high_resolution_limit.has_value());
    autoHighResSpot->setToolTip("Find spots as far as the detector reaches, instead of clipping the "
                                "detection at a fixed resolution. The high-resolution value is not used "
                                "while this is on.");
    auto *minPix = new NumberLineEdit(1.0f, 50.0f, static_cast<float>(min_pix_value_), 0, "px", this);
    auto *adaptiveMinPix = new QCheckBox("Adaptive min-pix (stills)", this);
    adaptiveMinPix->setChecked(adaptive_min_pix_);
    adaptiveMinPix->setToolTip("Choose the minimum pixels/spot per image: index the frame at min-pix "
                               "3/2/1 and keep whichever maximises indexed count x indexed fraction. "
                               "Stills only - a rotation dataset builds one lattice from all frames and "
                               "always uses the fixed min-pixels/spot value below.");
    // The same bounds DatasetSettings::MaxSpotCount enforces - offering more than it accepts only got
    // the value rejected further down.
    auto *maxSpots = new NumberLineEdit(10.0f, static_cast<float>(MAX_SPOT_COUNT),
                                        static_cast<float>(max_spots_), 0, "", this);
    spot->addRow("", adaptive);
    spot->addRow("Signal/noise", snr);
    spot->addRow("Photon count", count);
    spot->addRow("", autoHighResSpot);
    spot->addRow("High resolution [Å]", highResSpot);
    spot->addRow("", adaptiveMinPix);
    spot->addRow("Min pixels/spot", minPix);
    spot->addRow("Max spots/image", maxSpots);
    spotSection->setContentLayout(spot);
    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] {
        min_pix_value_ = std::llround(minPix->value()); EmitSpotFinding(); });
    connect(maxSpots, &NumberLineEdit::newValue, this, [this, maxSpots] {
        max_spots_ = std::llround(maxSpots->value()); EmitSpotFinding(); });
    // The adaptive finder sets its own threshold from each image's noise, so the signal/noise and
    // photon-count sliders do nothing while it is on - grey them out to make that clear.
    auto syncAdaptiveEnabled = [snr, count](bool on) {
        snr->setEnabled(!on);
        count->setEnabled(!on);
    };
    syncAdaptiveEnabled(spot_.adaptive_threshold);
    connect(adaptive, &QCheckBox::toggled, this, [this, syncAdaptiveEnabled](bool on) {
        spot_.adaptive_threshold = on;
        syncAdaptiveEnabled(on);
        EmitSpotFinding();
    });
    // An unset high-resolution limit (std::nullopt) means "to the detector edge", so the value is unused
    // while that is on - grey it out, as for the other automatic settings.
    auto syncHighResEnabled = [highResSpot](bool auto_on) { highResSpot->setEnabled(!auto_on); };
    syncHighResEnabled(!spot_.high_resolution_limit.has_value());
    connect(autoHighResSpot, &QCheckBox::toggled, this, [this, highResSpot, syncHighResEnabled](bool on) {
        if (on)
            spot_.high_resolution_limit = std::nullopt;
        else
            spot_.high_resolution_limit = static_cast<float>(highResSpot->value());
        syncHighResEnabled(on);
        EmitSpotFinding();
    });

    // The fixed min-pixels/spot field stays live even with adaptive min-pix on: it is what a rotation
    // dataset uses, and what stills fall back to when adaptive is switched off.
    connect(adaptiveMinPix, &QCheckBox::toggled, this, [this](bool on) {
        adaptive_min_pix_ = on;
        EmitSpotFinding();
    });

    return spotSection;
}

QWidget *JFJochViewerSettingsDock::BuildIndexingSection() {
    // Shared with the Grid page: a Grid run indexes every cell by default, with the same algorithm and
    // refinement choice an MX run uses. Whether it indexes at all is the Grid page's own switch
    // (GridScanAnalysisSettings::indexing); how it indexes is this section, for both modes.
    auto *idxSection = new CollapsibleSection("Indexing", this);
    auto *idx = new QFormLayout();
    idx->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    algo_ = new QComboBox(this);
    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(this);
    algoDesc_->setWordWrap(true);
    algoDesc_->setStyleSheet("color: gray;");
    auto *refine = new QComboBox(this);
    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())));
    idx->addRow("Algorithm", algo_);
    idx->addRow("", algoDesc_);
    idx->addRow("Refinement", refine);
    idxSection->setContentLayout(idx);
    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();
    });
    UpdateAlgorithmDescription();

    return idxSection;
}

QWidget *JFJochViewerSettingsDock::BuildMXPage() {
    // What is left after the four shared sections moved out is MX-only. A raster predicts nothing,
    // integrates nothing and merges nothing - the Grid job disables the process-H5, the merged output
    // and scaling alike - so Bragg integration, scaling and the reference dataset have no meaning
    // there and stay on this page.
    auto *page = new QWidget(this);
    auto *layout = new QVBoxLayout(page);
    layout->setContentsMargins(0, 0, 0, 0);

    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::BuildGoniometerSection() {
    // How the sample moved between images, in the same three cases a file stores: a rotation axis
    // (/entry/sample/transformations/omega), a grid scan (/entry/sample/grid_scan), or neither. The
    // mode IS the rotation/stills switch, so there is no second "process as stills" control, and it
    // is not tied to what the file says: a still file can be given an axis or a grid, and a rotation
    // file can be processed as stills by choosing Still.
    auto *section = new CollapsibleSection("Goniometer", this);
    auto *form = new QFormLayout();
    form->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);

    // Exclusive, so radio buttons rather than checkboxes: a dataset is one of the three, never two.
    modeStill_ = new QRadioButton("Still", this);
    modeStill_->setToolTip("The sample does not move between images: every image is an independent "
                           "still (per-frame indexing, fixed partiality).");
    modeRotation_ = new QRadioButton("Rotation", this);
    modeRotation_->setToolTip("The sample rotates between images: rotation indexing, Ewald-crossing "
                              "partiality and 3D rotation scaling.");
    modeGrid_ = new QRadioButton("Grid scan", this);
    modeGrid_->setToolTip("The sample translates between images on a raster. Processed as stills; the "
                          "grid is what the dataset-info panel maps the per-image results onto.");
    auto *modes = new QButtonGroup(this);
    modes->setExclusive(true);
    for (auto *b : {modeStill_, modeRotation_, modeGrid_})
        modes->addButton(b);
    modeStill_->setChecked(true);

    axisName_ = new QLineEdit(DEFAULT_AXIS_NAME, this);
    axisName_->setToolTip("Name of the rotated goniometer axis, as it is written to the output.");
    axisX_ = new NumberLineEdit(-1.0, 1.0, DEFAULT_AXIS[0], 3, "", this);
    axisY_ = new NumberLineEdit(-1.0, 1.0, DEFAULT_AXIS[1], 3, "", this);
    axisZ_ = new NumberLineEdit(-1.0, 1.0, DEFAULT_AXIS[2], 3, "", this);
    const QString axisTip = "Rotation axis in the laboratory frame (x, y, z); normalised on use.";
    for (auto *f : {axisX_, axisY_, axisZ_})
        f->setToolTip(axisTip);
    rotStart_ = new NumberLineEdit(-3600.0, 3600.0, 0.0, 3, "°", this);
    rotStart_->setToolTip("Angle of the first image.");
    rotIncrement_ = new NumberLineEdit(-10.0, 10.0, DEFAULT_INCREMENT_DEG, 3, "°", this);
    rotIncrement_->setToolTip("Angle rotated per image.");

    // Only the fast axis has a point count: the slow one is however many rows the images fill, which
    // is also why the file stores n_fast alone. The steps are signed - the sign is the direction the
    // scan runs in - so only zero is rejected.
    gridNFast_ = new NumberLineEdit(1.0, 100000.0, DEFAULT_GRID_N_FAST, 0, "", this);
    gridNFast_->setToolTip("Points along the fast axis. The number of slow rows follows from the "
                           "number of images.");
    gridStepX_ = new NumberLineEdit(-10000.0, 10000.0, DEFAULT_GRID_STEP_UM, 1, "μm", this);
    gridStepY_ = new NumberLineEdit(-10000.0, 10000.0, DEFAULT_GRID_STEP_UM, 1, "μm", this);
    const QString stepTip = "Distance between neighbouring points, in x and y. Negative = the scan "
                            "runs towards decreasing x / y.";
    gridStepX_->setToolTip(stepTip);
    gridStepY_->setToolTip(stepTip);
    gridVertical_ = new QCheckBox("Fast axis vertical", this);
    gridVertical_->setToolTip("The scan fills a column before moving to the next one (fast axis = y) "
                              "instead of filling a row (fast axis = x).");
    gridSnake_ = new QCheckBox("Snake scan", this);
    gridSnake_->setToolTip("Every second row/column is collected in the reverse direction (boustrophedon) "
                           "instead of returning to the start of the next one.");
    gridSummary_ = new QLabel(this);
    gridSummary_->setWordWrap(true);   // it carries a provenance line and, when set, a warning

    auto *axis = new QHBoxLayout();
    axis->addWidget(axisX_); axis->addWidget(axisY_); axis->addWidget(axisZ_);
    auto *step = new QHBoxLayout();
    step->addWidget(gridStepX_); step->addWidget(gridStepY_);
    auto *gridFlags = new QHBoxLayout();
    gridFlags->addWidget(gridVertical_); gridFlags->addWidget(gridSnake_);

    form->addRow("", modeStill_);
    form->addRow("", modeRotation_);
    form->addRow("Axis name", axisName_);
    form->addRow("Axis vector", axis);
    form->addRow("Start angle", rotStart_);
    form->addRow("Increment", rotIncrement_);
    form->addRow("", modeGrid_);
    form->addRow("Points (fast)", gridNFast_);
    form->addRow("Step x, y", step);
    form->addRow("", gridFlags);
    form->addRow("", gridSummary_);
    section->setContentLayout(form);

    EnableRotationFields(false);   // datasetLoaded picks the mode the file describes
    EnableGridFields(false);
    // One handler for the three: whichever is now on decides which fields are live, what the
    // experiment carries, and whether the run is a rotation or stills one.
    for (auto *b : {modeStill_, modeRotation_, modeGrid_})
        connect(b, &QRadioButton::toggled, this, [this](bool on) {
            if (!on)
                return;   // the button being switched off reports first; act once, on the new mode
            EnableRotationFields(modeRotation_->isChecked());
            EnableGridFields(modeGrid_->isChecked());
            UpdateGridSummary();
            ApplyProcessingMode();
            EmitExperiment();
        });
    connect(axisName_, &QLineEdit::editingFinished, this, [this] { EmitExperiment(); });
    for (auto *f : {axisX_, axisY_, axisZ_, rotStart_, rotIncrement_})
        connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });
    for (auto *f : {gridNFast_, gridStepX_, gridStepY_})
        connect(f, &NumberLineEdit::newValue, this, [this] { UpdateGridSummary(); EmitExperiment(); });
    for (auto *b : {gridVertical_, gridSnake_})
        connect(b, &QCheckBox::toggled, this, [this] { UpdateGridSummary(); EmitExperiment(); });

    return section;
}

void JFJochViewerSettingsDock::EnableRotationFields(bool on) {
    axisName_->setEnabled(on);
    for (auto *f : {axisX_, axisY_, axisZ_, rotStart_, rotIncrement_})
        f->setEnabled(on);
}

void JFJochViewerSettingsDock::EnableGridFields(bool on) {
    for (auto *f : {gridNFast_, gridStepX_, gridStepY_})
        f->setEnabled(on);
    gridVertical_->setEnabled(on);
    gridSnake_->setEnabled(on);
}

void JFJochViewerSettingsDock::UpdateGridSummary() {
    if (!modeGrid_->isChecked()) {
        gridSummary_->clear();
        MarkGridOverride(false);
        return;
    }
    const auto grid = GridScanFromFields();
    if (!grid) {
        // Refused rather than repaired with a plausible-looking value: a grid built on a step nobody
        // asked for puts every crystal somewhere else on the sample, and nothing about the map looks
        // wrong. With no grid set, a grid-scan run is refused instead.
        gridSummary_->setStyleSheet("color: #C0392B;");
        gridSummary_->setText("Step x and y must both be non-zero. No grid scan is set, so a grid-scan"
                              " run will be refused.");
        MarkGridOverride(true);
        return;
    }

    QString text = QStringLiteral("%1 x %2 points for %3 images")
                       .arg(grid->GetGridSizeX_step())
                       .arg(grid->GetGridSizeY_step())
                       .arg(experiment_.GetImageNum());

    // Same grid, said the same way: what the file stores is the point count, the steps and the two
    // flags - the row count is derived from the images and cannot differ on its own.
    const bool from_file = file_grid_.has_value()
        && file_grid_->GetNFast() == grid->GetNFast()
        && file_grid_->GetGridStepX_um() == grid->GetGridStepX_um()
        && file_grid_->GetGridStepY_um() == grid->GetGridStepY_um()
        && file_grid_->IsVerticalScan() == grid->IsVerticalScan()
        && file_grid_->IsSnakeScan() == grid->IsSnakeScan();
    if (from_file)
        text += "\nfrom the grid scan in the file";
    else if (file_grid_)
        text += "\nEDITED - this is not the grid scan the file describes";
    else
        text += "\nSET HERE - the file describes no grid scan";

    // The images have to fill the raster: a partly collected scan leaves the last row short, which is
    // legitimate, but a point count that does not divide the images is far more often a wrong one.
    const bool full_rows = grid->GetNElem() == experiment_.GetImageNum();
    if (!full_rows)
        text += QStringLiteral("\n%1 images do not fill %2 grid points - the last row is incomplete")
                    .arg(experiment_.GetImageNum()).arg(grid->GetNElem());

    gridSummary_->setStyleSheet(from_file && full_rows ? "color: gray;" : "color: #B8860B;");
    gridSummary_->setText(text);
    MarkGridOverride(!from_file);
}

void JFJochViewerSettingsDock::MarkGridOverride(bool on) {
    // An edited grid must not read like the file's. Getting one of these wrong reshapes the whole map
    // and moves every crystal it reports, and nothing else on screen changes, so the fields say so
    // themselves rather than leaving it to the summary line alone.
    const QString style = on ? "background-color: #FFF3CD;" : QString();
    for (auto *f : {gridNFast_, gridStepX_, gridStepY_})
        f->setStyleSheet(style);
    gridVertical_->setStyleSheet(style);
    gridSnake_->setStyleSheet(style);
}

std::optional<GoniometerAxis> JFJochViewerSettingsDock::GoniometerFromFields() const {
    if (!modeRotation_->isChecked())
        return std::nullopt;
    // GoniometerAxis throws on an empty name or a zero-length axis, and an exception thrown out of a
    // widget signal aborts the viewer - fall back to the defaults for a half-typed entry.
    std::string name = axisName_->text().trimmed().toStdString();
    if (name.empty())
        name = DEFAULT_AXIS_NAME;
    Coord axis(static_cast<float>(axisX_->value()), static_cast<float>(axisY_->value()),
               static_cast<float>(axisZ_->value()));
    if (axis.Length() == 0.0f)
        axis = Coord(DEFAULT_AXIS);
    GoniometerAxis gonio(name, static_cast<float>(rotStart_->value()),
                         static_cast<float>(rotIncrement_->value()), axis, gonioHelicalStep_);
    gonio.ScreeningWedge(gonioScreeningWedge_);
    return gonio;
}

std::optional<GridScanSettings> JFJochViewerSettingsDock::GridScanFromFields() const {
    if (!modeGrid_->isChecked())
        return std::nullopt;
    // GridScanSettings throws on a zero step or a non-positive point count, and an exception thrown
    // out of a widget signal aborts the viewer. Report "no grid" instead of substituting a value: a
    // grid on a step nobody entered is a map that is confidently in the wrong place, and the summary
    // says which field is at fault.
    const auto step_x = static_cast<float>(gridStepX_->value());
    const auto step_y = static_cast<float>(gridStepY_->value());
    const int64_t n_fast = std::llround(gridNFast_->value());
    if (step_x == 0.0f || step_y == 0.0f || n_fast < 1)
        return std::nullopt;
    GridScanSettings grid(n_fast, step_x, step_y,
                          gridSnake_->isChecked(), gridVertical_->isChecked());
    // The rows are however many the images fill, exactly as the reader does when a file carries a
    // grid: the file stores n_fast alone.
    grid.ImageNum(experiment_.GetImageNum());
    return grid;
}

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);

    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::BuildAzIntSection() {
    auto *azSection = new CollapsibleSection("Azimuthal integration", this);
    auto *az = new QFormLayout();
    az->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    auto *lowQ = new SliderPlusBox(1e-5, 10.0, 0.001, 4, this);
    lowQ->setValue(azint_.GetLowQ_recipA());
    auto *highQ = new SliderPlusBox(2e-5, 10.0, 0.001, 4, this);
    highQ->setValue(azint_.GetHighQ_recipA());
    auto *autoHighQ = new QCheckBox("To detector edge", this);
    autoHighQ->setChecked(!azint_.GetRequestedHighQ_recipA().has_value());
    autoHighQ->setToolTip("Integrate out to the highest Q the detector reaches. The high-Q value is not "
                          "used while this is on.");
    auto *spacing = new SliderPlusBox(1e-5, 1.0, 0.001, 5, this, SliderPlusBox::ScaleType::Logarithmic);
    spacing->setValue(azint_.GetQSpacing_recipA());
    auto *azimBins = new QComboBox(this);
    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("", autoHighQ);
    az->addRow("High Q [Å⁻¹]", highQ);
    az->addRow("Q spacing [Å⁻¹]", spacing);
    az->addRow("Azimuthal bins", azimBins);
    azSection->setContentLayout(az);

    auto emitAz = [=, this] {
        azint_.QRange_recipA(static_cast<float>(lowQ->value()),
                             autoHighQ->isChecked() ? std::nullopt
                                                    : std::optional<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(); });
    connect(autoHighQ, &QCheckBox::toggled, this, [emitAz, highQ](bool on) {
        highQ->setEnabled(!on);
        emitAz();
    });
    highQ->setEnabled(!autoHighQ->isChecked());

    return azSection;
}

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

    // The powder-calibration widget is the whole page: it already carries the calibrant and the two
    // interactive (current-image) fits, and it now also carries the method a whole-dataset run uses,
    // so the interactive and dataset paths share one calibrant selection.
    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_);

    // The rings method reads the ring's position at every azimuth, so the run has to be integrated in
    // azimuthal sectors; one sector is a plain radial profile and cannot locate the ring. The sector
    // count is the azimuthal-integration section above - say here when it is set too low to fit with.
    auto *bins = new QLabel(page);
    bins->setWordWrap(true);
    bins->setStyleSheet("color: gray;");
    powderLayout->addWidget(bins);
    powderSection->setContentLayout(powderLayout);
    layout->addWidget(powderSection);

    auto refreshBins = [this, bins] {
        bins->setText(azint_.GetAzimuthalBinCount() < 4
                          ? QStringLiteral("Rings method: too few azimuthal bins (%1) to locate a ring;"
                                           " the run will use 32.").arg(azint_.GetAzimuthalBinCount())
                          : QString());
    };
    refreshBins();
    connect(this, &JFJochViewerSettingsDock::azintChanged, this, [refreshBins] { refreshBins(); });

    layout->addStretch();
    return page;
}

QWidget *JFJochViewerSettingsDock::BuildGridPage() {
    // The Grid page is the raster analysis and nothing else: where the crystals are is decided from
    // the finished map, and these are the knobs of that decision. The same settings are offered by the
    // broker frontend (frontend/src/components/GridScanAnalysisSettings.tsx); the wording, the order
    // and the units follow it, and every default is read out of GridScanAnalysisSettings rather than
    // written again here, so the two panels cannot drift apart on what a default is.
    auto *page = new QWidget(this);
    auto *layout = new QVBoxLayout(page);
    layout->setContentsMargins(0, 0, 0, 0);

    const GridScanAnalysisSettings defaults;

    auto *blobSection = new CollapsibleSection("Which cells are a crystal", page);
    auto *blob = new QFormLayout();
    blob->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    proteinScore_ = new NumberLineEdit(0.0f, 1.0f, defaults.GetProteinScoreThreshold(), 2, "", page);
    proteinScore_->setToolTip("The per-image protein score saturates, so this only has to separate "
                              "\"something diffracted here\" from \"nothing did\".");
    growScore_ = new NumberLineEdit(0.0f, 1.0f, defaults.GetGrowScoreThreshold(), 2, "", page);
    growScore_->setToolTip("Once a patch has a cell above the threshold it is grown out to this score, "
                           "so one weak cell does not split a crystal in two. Growth cannot start a "
                           "patch on its own.");
    minBlobCells_ = new NumberLineEdit(1.0f, 10000.0f, static_cast<float>(defaults.GetMinBlobCells()),
                                       0, "", page);
    minBlobCells_->setToolTip("Two cells can be the two ends of a single hit on a cell boundary; three "
                              "is the smallest patch that is a shape rather than a coincidence.");
    decisiveScore_ = new NumberLineEdit(0.0f, 1.0f, defaults.GetDecisiveSingleCellScore(), 2, "", page);
    decisiveScore_->setToolTip("One cell scoring this high is a crystal on its own - a crystal smaller "
                               "than the grid step lights exactly one cell. Keep it well above the "
                               "protein score threshold.");
    blob->addRow("Protein score threshold", proteinScore_);
    blob->addRow("Grow score threshold", growScore_);
    blob->addRow("Minimum cells per crystal", minBlobCells_);
    blob->addRow("Decisive single-cell score", decisiveScore_);
    blobSection->setContentLayout(blob);
    layout->addWidget(blobSection);

    auto *reportSection = new CollapsibleSection("Reporting and indexing", page);
    auto *report = new QFormLayout();
    report->setFieldGrowthPolicy(QFormLayout::AllNonFixedFieldsGrow);
    // No cap is the default, and it is spelled as the box being unticked rather than as a count that
    // happens to mean "all": a crystal that was found and then dropped cannot be got back, so the
    // setting that drops them has to be switched on deliberately.
    maxCrystalsOn_ = new QCheckBox("Limit crystals reported", page);
    maxCrystalsOn_->setChecked(defaults.GetMaxCrystals().has_value());
    maxCrystalsOn_->setToolTip("Unticked, every crystal found is reported. Tick it for a loop full of "
                               "shards that would otherwise be labelled by the dozen.");
    maxCrystals_ = new NumberLineEdit(1.0f, 10000.0f,
                                      static_cast<float>(defaults.GetMaxCrystals().value_or(10)), 0, "", page);
    maxCrystals_->setEnabled(maxCrystalsOn_->isChecked());
    maxCrystals_->setToolTip("Crystals are sorted by score, so this keeps the best.");
    gridIndexing_ = new QCheckBox("Index each raster cell", page);
    gridIndexing_->setChecked(defaults.IsIndexing());
    gridIndexing_->setToolTip("Additive: crystals are still found on the protein score, so indexing "
                              "only adds what was found in them. Turn it off for a very large raster "
                              "where the GPU is the constraint.");
    // Checkbox and value on one line in the field column, as the scaling section's resolution limits.
    auto *maxRow = new QHBoxLayout();
    maxRow->addWidget(maxCrystalsOn_);
    maxRow->addWidget(maxCrystals_, 1);
    report->addRow("", maxRow);
    report->addRow("", gridIndexing_);
    reportSection->setContentLayout(report);
    layout->addWidget(reportSection);

    for (auto *f : {proteinScore_, growScore_, minBlobCells_, decisiveScore_, maxCrystals_})
        connect(f, &NumberLineEdit::newValue, this, [this] { EmitExperiment(); });
    connect(maxCrystalsOn_, &QCheckBox::toggled, this, [this](bool on) {
        maxCrystals_->setEnabled(on);
        EmitExperiment();
    });
    connect(gridIndexing_, &QCheckBox::toggled, this, [this] { EmitExperiment(); });

    layout->addStretch();
    return page;
}

GridScanAnalysisSettings JFJochViewerSettingsDock::GridAnalysisFromFields() const {
    GridScanAnalysisSettings settings;
    settings.ProteinScoreThreshold(static_cast<float>(proteinScore_->value()))
            .GrowScoreThreshold(static_cast<float>(growScore_->value()))
            .MinBlobCells(std::llround(minBlobCells_->value()))
            .DecisiveSingleCellScore(static_cast<float>(decisiveScore_->value()))
            .MaxCrystals(maxCrystalsOn_->isChecked()
                             ? std::optional<int64_t>(std::llround(maxCrystals_->value()))
                             : std::nullopt)
            .Indexing(gridIndexing_->isChecked());
    return settings;
}

void JFJochViewerSettingsDock::SyncMinPix() {
    // Per-image min-pix indexes each frame on its own, which only means something for stills; rotation
    // indexing builds one lattice from all frames, so it keeps the fixed value.
    spot_.min_pix_per_spot = (adaptive_min_pix_ && !indexing_.GetRotationIndexing())
                                 ? std::optional<int64_t>()
                                 : std::optional<int64_t>(min_pix_value_);
}

void JFJochViewerSettingsDock::EmitSpotFinding() {
    SyncMinPix();
    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);
    // Background trim: use the old symmetric trimmed mean for the r2..r3 ring (drop the lowest and
    // highest fraction of ring pixels) in place of the default high-side sigma clip. Setting the trim
    // clears the clip, so unchecked simply leaves the default estimator in place.
    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 instead of the default high-side sigma clip. A symmetric trim "
                        "is biased low on Poisson data and adds a few counts to every partial, so this "
                        "is for back compatibility; unchecked = the 4 sigma clip.");
    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("", trimRow);
    section->setContentLayout(form);

    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()));
        // Either estimator clears the other, so unchecking has to put the default clip back explicitly.
        if (bkgTrim->isChecked())
            bragg_.BackgroundTrimFraction(static_cast<float>(bkgTrimFrac->value()));
        else
            bragg_.BackgroundClipNSigma(BraggIntegrationSettings().GetBackgroundClipNSigma());
        emit braggChanged(bragg_);
    };
    connect(gaussian, &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 the rotation axis (goniometer
    // 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 *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 *partRefine = new QCheckBox("Partiality post-refinement (stills)", this);
    partRefine->setChecked(scaling_.GetStillsPartialityRefine());
    partRefine->setToolTip("Stills: refine a per-crystal orientation tilt against the running merge and "
                           "recompute each reflection's partiality (physical Ewald-proximity model), then "
                           "re-scale/merge. On by default; uncheck for the simple model (each reflection a "
                           "full, single-pass). No effect on rotation data.");
    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());
    auto *limitLowRes = new QCheckBox("Low-resolution limit", this);
    limitLowRes->setChecked(scaling_.GetLowResolutionLimit_A().has_value());
    limitLowRes->setToolTip("Drop reflections coarser than this from scaling and merging. They sit behind "
                            "or beside the beam stop and are measured on a background it has eaten into. "
                            "On by default at 50 Å, the value XDS configurations use.");
    auto *lowRes = new NumberLineEdit(5.0f, 500.0f, scaling_.GetLowResolutionLimit_A().value_or(50.0), 1, "Å", this);
    lowRes->setEnabled(limitLowRes->isChecked());

    form->addRow("", friedel);
    form->addRow("", corrections);
    form->addRow("", partRefine);
    // 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 *lowResRow = new QHBoxLayout();
    lowResRow->addWidget(limitLowRes);
    lowResRow->addWidget(lowRes, 1);
    form->addRow("", lowResRow);
    section->setContentLayout(form);

    auto emitScaling = [=, this] {
        scaling_.MergeFriedel(friedel->isChecked());
        scaling_.CorrectionSurfaces(corrections->isChecked());
        scaling_.StillsPartialityRefine(partRefine->isChecked());
        scaling_.HighResolutionLimit_A(limitRes->isChecked()
            ? std::optional<double>(highRes->value()) : std::nullopt);
        scaling_.LowResolutionLimit_A(limitLowRes->isChecked()
            ? std::optional<double>(lowRes->value()) : std::nullopt);
        emit scalingChanged(scaling_);
    };
    connect(friedel, &QCheckBox::toggled, this, [emitScaling] { emitScaling(); });
    connect(corrections, &QCheckBox::toggled, this, [emitScaling] { emitScaling(); });
    connect(partRefine, &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(limitLowRes, &QCheckBox::toggled, this, [emitScaling, lowRes](bool on) {
        lowRes->setEnabled(on); emitScaling(); });
    connect(lowRes, &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));
    experiment_.PolarizationFactor(polarizationOn_->isChecked()
        ? std::optional<float>(static_cast<float>(polarization_->value())) : std::nullopt);
    experiment_.Goniometer(GoniometerFromFields());
    experiment_.GridScan(GridScanFromFields());
    experiment_.ImportGridScanAnalysisSettings(GridAnalysisFromFields());
    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 polarization = experiment_.GetPolarizationFactor();
    QSignalBlocker blockPolarization(polarizationOn_);
    polarizationOn_->setChecked(polarization.has_value());
    polarization_->setEnabled(polarization.has_value());
    if (polarization)
        polarization_->setValue(polarization.value());

    // The mode follows what the experiment describes, and the described one's fields are filled from
    // it. The other two keep what they show - the generic defaults, or what the user last entered -
    // so switching away and back does not lose an axis or a grid.
    const auto gonio = experiment_.GetGoniometer();
    const auto grid = experiment_.GetGridScan();
    QSignalBlocker blockStill(modeStill_), blockRotation(modeRotation_), blockGrid(modeGrid_);
    // Which of the three the panel shows. Two things decide it, and neither is obvious.
    //
    // A grid scan is stored WITH a spindle beside it - NXmx cannot say "no rotation", so a raster
    // carries a stationary omega - so a goniometer that does not scan must not outrank the grid.
    // Read the other way round, the panel flipped to Rotation the moment a grid-scan run came back
    // carrying that placeholder axis, and the next edit then dropped the raster from the experiment
    // and got the following run refused.
    //
    // And a grid the fields cannot make - a step typed to zero - leaves the experiment with no grid
    // scan at all. That is a half-finished edit, not a dataset that stopped being a raster, so the
    // mode stays where the user put it and the summary says what is wrong. Anything else (a file that
    // simply has no grid) does move the mode.
    const bool grid_mode = grid.has_value()
        ? !(gonio.has_value() && gonio->IsScanning())
        : (modeGrid_->isChecked() && !GridScanFromFields().has_value());
    modeGrid_->setChecked(grid_mode);
    modeRotation_->setChecked(!grid_mode && gonio.has_value());
    modeStill_->setChecked(!grid_mode && !gonio.has_value());
    EnableRotationFields(modeRotation_->isChecked());
    EnableGridFields(grid_mode);
    if (gonio) {
        axisName_->setText(QString::fromStdString(gonio->GetName()));
        axisX_->setValue(gonio->GetAxis().x);
        axisY_->setValue(gonio->GetAxis().y);
        axisZ_->setValue(gonio->GetAxis().z);
        rotStart_->setValue(gonio->GetStart_deg());
        rotIncrement_->setValue(gonio->GetIncrement_deg());
        gonioHelicalStep_ = gonio->GetHelicalStep();
        gonioScreeningWedge_ = gonio->GetScreeningWedge();
    }
    if (grid) {
        gridNFast_->setValue(grid->GetNFast());
        gridStepX_->setValue(grid->GetGridStepX_um());
        gridStepY_->setValue(grid->GetGridStepY_um());
        QSignalBlocker blockVertical(gridVertical_), blockSnake(gridSnake_);
        gridVertical_->setChecked(grid->IsVerticalScan());
        gridSnake_->setChecked(grid->IsSnakeScan());
    }
    UpdateGridSummary();

    // The grid-scan analysis settings come back the same way the geometry does, so what the panel
    // shows is always what a run would use: the panel writes them onto the experiment, the reader
    // carries them on the dataset (JFJochReader::UpdateGeomMetadata), and this reads them back.
    const auto analysis = experiment_.GetGridScanAnalysisSettings();
    proteinScore_->setValue(analysis.GetProteinScoreThreshold());
    growScore_->setValue(analysis.GetGrowScoreThreshold());
    minBlobCells_->setValue(static_cast<float>(analysis.GetMinBlobCells()));
    decisiveScore_->setValue(analysis.GetDecisiveSingleCellScore());
    QSignalBlocker blockMaxCrystals(maxCrystalsOn_), blockIndexing(gridIndexing_);
    maxCrystalsOn_->setChecked(analysis.GetMaxCrystals().has_value());
    maxCrystals_->setEnabled(analysis.GetMaxCrystals().has_value());
    if (analysis.GetMaxCrystals())
        maxCrystals_->setValue(static_cast<float>(analysis.GetMaxCrystals().value()));
    gridIndexing_->setChecked(analysis.IsIndexing());

    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();
    ApplyProcessingMode();   // the mode just read back decides rotation vs stills
}

void JFJochViewerSettingsDock::fileOpened() {
    // The baseline the grid fields are called edited against. It can only be taken here: datasetLoaded
    // fires again after every settings change - the panel's own experiment comes back through the
    // reader - and by then the file's grid scan is indistinguishable from one typed over it.
    file_grid_ = experiment_.GetGridScan();
    UpdateGridSummary();
}

void JFJochViewerSettingsDock::ApplyProcessingMode() {
    // Rotation is the only mode that changes how the data is processed: the rotation good-path
    // (rotation indexing + Ewald partiality + rot3d combine + scale-fulls). A grid scan is a raster
    // of stills, so it runs exactly as Still does.
    const bool rotation_mode = modeRotation_ && modeRotation_->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);
    }
}