Jungfraujoch/viewer/windows/JFJochProcessingJobsWindow.cpp

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

#include "JFJochProcessingJobsWindow.h"
#include "JFJochMergeStatsWindow.h"
#include "../widgets/ToolbarIcons.h"
#include "../../rugnux/RugnuxCommandLine.h"

#include <QApplication>
#include <QCheckBox>
#include <QClipboard>
#include <QComboBox>
#include <QDateTime>
#include <QDialog>
#include <QDir>
#include <QFont>
#include <QIcon>
#include <QDialogButtonBox>
#include <QFileInfo>
#include <QFormLayout>
#include <QHeaderView>
#include <QLabel>
#include <QLineEdit>
#include <QMessageBox>
#include <QProgressBar>
#include <QPushButton>
#include <QSpinBox>
#include <QStackedWidget>
#include <QStyle>
#include <QPainter>
#include <QPixmap>
#include <QTableWidget>
#include <QToolBar>
#include <QToolButton>
#include <QVBoxLayout>

#include <thread>

namespace {
    // Status (the progress bar) is column 2 so it stays visible in the narrow dock.
    enum Column { COL_NAME = 0, COL_STATUS, COL_STARTED, COL_MODE, COL_IMAGES, COL_INDEX, COL_CELL, COL_ACTIONS, COL_COUNT };

    int default_threads() {
        const unsigned hc = std::thread::hardware_concurrency();
        return hc == 0 ? 4 : static_cast<int>(hc);
    }

    QTableWidgetItem *fixedItem(const QString &text) {   // a non-editable cell
        auto *cell = new QTableWidgetItem(text);
        cell->setFlags(cell->flags() & ~Qt::ItemIsEditable);
        return cell;
    }
}

JFJochProcessingJobsWindow::JFJochProcessingJobsWindow(JFJochImageReadingWorker *worker, QWidget *parent)
    : QWidget(parent), worker_(worker) {
    setWindowTitle("Processing");

    controller_ = new JFJochProcessController(this);
    connect(controller_, &JFJochProcessController::phaseChanged, this, &JFJochProcessingJobsWindow::onPhase);
    connect(controller_, &JFJochProcessController::progress, this, &JFJochProcessingJobsWindow::onProgress);
    connect(controller_, &JFJochProcessController::finished, this, &JFJochProcessingJobsWindow::onFinished);
    connect(controller_, &JFJochProcessController::failed, this, &JFJochProcessingJobsWindow::onFailed);
    connect(controller_, &JFJochProcessController::liveDataset, this, &JFJochProcessingJobsWindow::liveDataset);

    toolbar_ = new QToolBar("Jobs", this);
    toolbar_->setMovable(false);
    // "New job" is launched by the "Reanalyze dataset" hero button, not from this dock's toolbar.
    toolbar_->addAction("Cancel", this, &JFJochProcessingJobsWindow::cancelJob);
    toolbar_->addSeparator();
    toolbar_->addAction("Show selected", this, &JFJochProcessingJobsWindow::viewResults);

    table_ = new QTableWidget(0, COL_COUNT, this);
    table_->setMinimumHeight(60);   // let the bottom dock shrink freely
    table_->setHorizontalHeaderLabels({"Name", "Status", "Started", "Mode", "Images", "Index %", "Unit cell", ""});
    table_->horizontalHeader()->setStretchLastSection(false);
    table_->horizontalHeader()->setSectionResizeMode(COL_CELL, QHeaderView::Stretch);
    table_->horizontalHeader()->setSectionResizeMode(COL_ACTIONS, QHeaderView::Fixed);
    table_->setColumnWidth(COL_ACTIONS, 56);
    table_->setSelectionBehavior(QAbstractItemView::SelectRows);
    table_->setSelectionMode(QAbstractItemView::SingleSelection);
    // Only the Name column is editable (per-item flags); editing it renames the run's legend label.
    table_->setEditTriggers(QAbstractItemView::DoubleClicked | QAbstractItemView::EditKeyPressed);
    connect(table_, &QTableWidget::itemChanged, this, [this](QTableWidgetItem *item) {
        if (item->column() != COL_NAME)
            return;
        const int row = item->row();
        if (row < 0 || row >= static_cast<int>(jobs_.size()) || item->text() == jobs_[row].label)
            return;
        jobs_[row].label = item->text();
        emit renameRun(jobs_[row].id, jobs_[row].label);
    });
    // Double-click a row (other than its editable Name) to show that run in the plots/image.
    connect(table_, &QTableWidget::cellDoubleClicked, this, [this](int row, int col) {
        if (col == COL_NAME)
            return;   // double-clicking Name edits the label
        if (row >= 0 && row < static_cast<int>(jobs_.size()) && jobs_[row].has_result)
            emit activateSnapshot(jobs_[row].id);
    });

    auto *message = new QLabel("Dataset re-processing is currently available only in File mode.\n\n"
                               "Open a stored HDF5 file to run processing jobs.", this);
    message->setAlignment(Qt::AlignCenter);
    message->setWordWrap(true);

    stack_ = new QStackedWidget(this);
    stack_->addWidget(table_);     // page 0
    stack_->addWidget(message);    // page 1

    auto *layout = new QVBoxLayout(this);
    layout->setContentsMargins(0, 0, 0, 0);
    layout->addWidget(toolbar_);
    layout->addWidget(stack_);
}

void JFJochProcessingJobsWindow::onHttpConnectionChanged(bool connected, QString addr) {
    // Re-processing reads a stored HDF5 file; it is not available for the live HTTP stream.
    stack_->setCurrentIndex(connected ? 1 : 0);
    toolbar_->setEnabled(!connected);
}

int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec &spec, bool azint) {
    QDialog dlg(window());   // centre on the main window, not inside the processing dock
    // The kind of job (MX full analysis vs azimuthal integration) comes from the panel's MX/AzInt
    // toggle, so the dialog only collects the run options.
    dlg.setWindowTitle(azint ? "New azimuthal-integration job" : "New full-analysis job");

    auto *start_image = new QSpinBox(&dlg);
    start_image->setRange(0, 1'000'000'000);
    start_image->setValue(0);

    auto *end_image = new QSpinBox(&dlg);
    end_image->setRange(0, 1'000'000'000);
    end_image->setValue(0);
    end_image->setSpecialValueText("end");   // 0 => to the last image

    auto *threads = new QSpinBox(&dlg);
    threads->setRange(1, 256);
    threads->setValue(default_threads());

    // Two independent outputs: the large per-image _process.h5 (updates the viewer with spots/results)
    // and the small merged .mtz/.cif. Either can be turned off; the ISa/R-meas window is shown
    // regardless (it needs only the in-memory merge statistics), so a stats-only run turns both off.
    auto *save_h5 = new QCheckBox("Save _process.h5 (per-image results; updates viewer)", &dlg);
    save_h5->setChecked(true);

    auto *save_merged = new QCheckBox("Write merged .mtz/.cif", &dlg);
    save_merged->setChecked(true);
    save_merged->setEnabled(!azint);   // no merged output in azimuthal-integration mode

    // Default the output next to the input file, not the viewer's working directory (the viewer starts
    // wherever it was installed). This is an absolute path; Rugnux writes it via the trusted setter,
    // and toNativeSeparators keeps a UNC/Windows path openable afterwards.
    const QFileInfo fi(inputs.file);
    const QString stem = fi.completeBaseName().remove(QStringLiteral("_master"));
    const QString default_prefix = QDir::toNativeSeparators(
        QStringLiteral("%1/%2_run%3").arg(fi.absolutePath(), stem).arg(job_counter_ + 1));
    auto *prefix = new QLineEdit(default_prefix, &dlg);

    // Rotation-vs-stills mode (rotation indexing + partiality + rot3d) is set in the settings panel via
    // "Process as stills"; the dialog only collects run options. Scaling applies to MX full analysis.
    auto *scaling = new QCheckBox("Scale && merge", &dlg);
    scaling->setChecked(true);
    scaling->setEnabled(!azint);

    auto *form = new QFormLayout;
    form->addRow("Start image", start_image);
    form->addRow("End image", end_image);
    form->addRow("Threads", threads);
    form->addRow(save_h5);
    form->addRow(save_merged);
    form->addRow("Output prefix", prefix);
    form->addRow(scaling);

    int result = 0;
    auto *run = new QPushButton("Run locally", &dlg);
    auto *copy = new QPushButton("Copy command", &dlg);
    auto *cancel = new QPushButton("Cancel", &dlg);
    run->setDefault(true);
    connect(run, &QPushButton::clicked, &dlg, [&] { result = 1; dlg.accept(); });
    connect(copy, &QPushButton::clicked, &dlg, [&] { result = 2; dlg.accept(); });
    connect(cancel, &QPushButton::clicked, &dlg, [&] { result = 0; dlg.reject(); });

    auto *buttons = new QHBoxLayout;
    buttons->addStretch();
    buttons->addWidget(run);
    buttons->addWidget(copy);
    buttons->addWidget(cancel);

    auto *layout = new QVBoxLayout(&dlg);
    layout->addLayout(form);
    layout->addLayout(buttons);

    dlg.exec();
    if (result != 0) {
        spec.mode = azint ? ProcessMode::AzimuthalIntegration : ProcessMode::FullAnalysis;
        spec.start_image = start_image->value();
        spec.end_image = end_image->value();
        spec.threads = threads->value();
        spec.save_h5 = save_h5->isChecked();
        spec.save_merged = save_merged->isEnabled() && save_merged->isChecked();
        spec.prefix = prefix->text();
        spec.scaling = scaling->isEnabled() && scaling->isChecked();
    }
    return result;
}

ProcessConfig JFJochProcessingJobsWindow::buildConfig(const JobSpec &spec, const ReprocessingInputs &inputs) const {
    ProcessConfig config;
    config.mode = spec.mode;
    config.nthreads = spec.threads;
    config.start_image = spec.start_image;
    config.end_image = spec.end_image > 0 ? spec.end_image : -1;   // 0 => to the end
    // Files land at output_prefix; leave it empty (write nothing, stats only) when neither output is
    // wanted. The two flags then select which files are actually written there.
    config.output_prefix = (spec.save_h5 || spec.save_merged) ? spec.prefix.toStdString() : std::string();
    config.write_process_h5 = spec.save_h5;
    config.write_merged = spec.save_merged;
    config.spot_finding = inputs.spot_finding;
    if (spec.mode == ProcessMode::FullAnalysis) {
        // Rotation indexing follows the panel's "Process as stills" (= the experiment's indexing
        // setting); a rotation run uses 60 first-pass images to find the lattice.
        config.rotation_indexing = inputs.experiment.GetIndexingSettings().GetRotationIndexing();
        config.two_pass_rotation = true;
        if (config.rotation_indexing)
            config.rotation_indexing_image_count = 60;
        config.run_scaling = spec.scaling;
        config.reference_data = inputs.reference_data;   // enables CCref / reference-based scaling
    }
    return config;
}

void JFJochProcessingJobsWindow::newJob(bool azint) {
    const ReprocessingInputs inputs = worker_->GetReprocessingInputs();
    if (!inputs.valid) {
        QMessageBox::information(this, "Processing", "Open a file first (processing is not available for live HTTP data).");
        return;
    }

    JobSpec spec;
    const int action = askJob(inputs, spec, azint);
    if (action == 0)
        return;

    const ProcessConfig config = buildConfig(spec, inputs);

    // The experiment already carries the panel's indexing settings — including RotationIndexing set by
    // "Process as stills" (needed so IndexAndRefine builds a rotation indexer) — so it is used as-is.
    const DiffractionExperiment &experiment = inputs.experiment;

    if (action == 2) {   // copy command line
        const QString cmd = QString::fromStdString(
            RugnuxCommandLine(config, experiment, inputs.file.toStdString()));
        QApplication::clipboard()->setText(cmd);
        QMessageBox::information(this, "Command line", cmd + "\n\n(copied to clipboard)");
        return;
    }

    if (controller_->running()) {
        QMessageBox::information(this, "Processing", "A job is already running; wait for it to finish or cancel it.");
        return;
    }

    const bool full = spec.mode == ProcessMode::FullAnalysis;
    const int run_number = ++job_counter_;
    const QString label = QStringLiteral("%1 %2").arg(full ? "Full" : "AzInt").arg(run_number);
    const QString id = QStringLiteral("run-%1").arg(run_number);

    JobInfo info;
    info.id = id;
    info.label = label;
    if (spec.save_h5)
        info.snapshot_path = QString::fromStdString(config.output_prefix) + "_process.h5";

    const int row = table_->rowCount();
    table_->insertRow(row);
    jobs_.push_back(info);   // jobs_[row] must exist before setItem(COL_NAME) fires itemChanged

    const QString range_text = (spec.start_image == 0 && spec.end_image == 0)
        ? QStringLiteral("all")
        : QStringLiteral("%1–%2").arg(spec.start_image)
              .arg(spec.end_image > 0 ? QString::number(spec.end_image) : QStringLiteral("end"));
    const int expected = spec.end_image > spec.start_image ? spec.end_image - spec.start_image : 0;

    table_->setItem(row, COL_NAME, new QTableWidgetItem(label));   // editable (default flags)
    table_->setItem(row, COL_STARTED, fixedItem(QDateTime::currentDateTime().toString("HH:mm:ss")));
    table_->setItem(row, COL_MODE, fixedItem(full ? "Full" : "AzInt"));
    table_->setItem(row, COL_IMAGES, fixedItem(range_text));
    table_->setItem(row, COL_STATUS, fixedItem("queued"));
    table_->setItem(row, COL_INDEX, fixedItem("-"));
    table_->setItem(row, COL_CELL, fixedItem("-"));
    addRowActions(row, id);

    // A progress bar lives in the Status cell while the job runs; it shows the phase as text until
    // image processing starts, then "<done> / <expected>" with the bar filling in the background.
    running_bar_ = new QProgressBar(table_);
    running_bar_->setAlignment(Qt::AlignCenter);
    running_bar_->setRange(0, expected > 0 ? expected : 1);
    running_bar_->setValue(0);
    running_bar_->setFormat("queued");
    table_->setCellWidget(row, COL_STATUS, running_bar_);

    running_row_ = row;

    job_timer_.start();
    controller_->start(inputs.file, experiment, inputs.pixel_mask, config);
    emit jobStarted();
    emit writeStatusBar("Started processing job " + label);
}

void JFJochProcessingJobsWindow::cancelJob() {
    if (controller_->running()) {
        controller_->cancel();
        emit writeStatusBar("Cancelling processing job…");
    }
}

void JFJochProcessingJobsWindow::removeResult() {
    const int row = table_->currentRow();
    if (row < 0 || row >= static_cast<int>(jobs_.size()))
        return;
    if (jobs_[row].id == "Original")
        return;   // the original file is always kept
    if (row == running_row_) {
        QMessageBox::information(this, "Processing", "Cancel the running job before removing it.");
        return;
    }
    emit removeRun(jobs_[row].id);   // drops the snapshot from the reader

    QSignalBlocker block(table_);    // row removal must not look like a rename
    table_->removeRow(row);
    jobs_.erase(jobs_.begin() + row);
    if (running_row_ > row)
        --running_row_;
}

void JFJochProcessingJobsWindow::addRowActions(int row, const QString &id) {
    auto *w = new QWidget(table_);
    auto *l = new QHBoxLayout(w);
    l->setContentsMargins(2, 0, 2, 0);
    l->setSpacing(2);

    auto *graph = new QToolButton(w);
    graph->setIcon(ToolbarIcons::linePlot());
    graph->setAutoRaise(true);
    graph->setToolTip("Show merge statistics");
    graph->setEnabled(false);   // enabled once a scaling/merging result arrives for this run
    connect(graph, &QToolButton::clicked, this, [this, id] { showStats(id); });

    auto *trash = new QToolButton(w);
    trash->setIcon(style()->standardIcon(QStyle::SP_TrashIcon));
    trash->setAutoRaise(true);
    trash->setToolTip("Remove this run");
    trash->setEnabled(id != "Original");   // the original file is always kept
    connect(trash, &QToolButton::clicked, this, [this, id] { removeRunById(id); });

    l->addWidget(graph);
    l->addWidget(trash);
    table_->setCellWidget(row, COL_ACTIONS, w);
    jobs_[row].graph_btn = graph;
}

void JFJochProcessingJobsWindow::showStats(const QString &id) {
    for (const auto &j: jobs_) {
        if (j.id == id && j.has_merge_stats) {
            auto *win = new JFJochMergeStatsWindow(j.label, j.merge_stats, j.isa, j.merge_has_reference,
                                                   j.twinning, j.space_group_number, j.space_group_search,
                                                   window());
            win->show();
            return;
        }
    }
}

void JFJochProcessingJobsWindow::removeRunById(const QString &id) {
    for (int row = 0; row < static_cast<int>(jobs_.size()); ++row) {
        if (jobs_[row].id != id)
            continue;
        if (id == "Original")
            return;
        if (row == running_row_) {
            QMessageBox::information(this, "Processing", "Cancel the running job before removing it.");
            return;
        }
        emit removeRun(id);
        QSignalBlocker block(table_);
        table_->removeRow(row);
        jobs_.erase(jobs_.begin() + row);
        if (running_row_ > row)
            --running_row_;
        return;
    }
}

void JFJochProcessingJobsWindow::clearJobs() {
    if (controller_->running())
        controller_->cancel();
    emit liveDataset(nullptr);

    QSignalBlocker block(table_);
    table_->setRowCount(0);
    jobs_.clear();
    job_counter_ = 0;
    running_row_ = -1;
    running_bar_ = nullptr;
    addOriginalRow();
}

void JFJochProcessingJobsWindow::addOriginalRow() {
    // The file's own data, listed as the first run so it can be shown like any reprocessing run.
    JobInfo info;
    info.id = "Original";
    info.label = "Original";
    info.has_result = true;

    const int row = table_->rowCount();
    table_->insertRow(row);
    jobs_.push_back(info);

    QSignalBlocker block(table_);
    table_->setItem(row, COL_NAME, fixedItem("Original"));   // reserved name, not editable
    table_->setItem(row, COL_STATUS, fixedItem(""));
    table_->setItem(row, COL_STARTED, fixedItem("—"));
    table_->setItem(row, COL_MODE, fixedItem("HDF5"));
    table_->setItem(row, COL_IMAGES, fixedItem("all"));
    table_->setItem(row, COL_INDEX, fixedItem("-"));
    table_->setItem(row, COL_CELL, fixedItem("-"));
    addRowActions(row, info.id);
}

void JFJochProcessingJobsWindow::setActiveRun(QString active_id) {
    QSignalBlocker block(table_);
    for (int row = 0; row < static_cast<int>(jobs_.size()); row++) {
        auto *item = table_->item(row, COL_NAME);
        if (!item)
            continue;
        QFont f = item->font();
        f.setBold(jobs_[row].id == active_id);
        item->setFont(f);
    }
}

void JFJochProcessingJobsWindow::viewResults() {
    const int row = table_->currentRow();
    if (row < 0 || row >= static_cast<int>(jobs_.size()))
        return;
    if (!jobs_[row].has_result) {
        QMessageBox::information(this, "Processing", "This job has no saved results to view.");
        return;
    }
    emit activateSnapshot(jobs_[row].id);
}

void JFJochProcessingJobsWindow::setStatus(int row, const QString &text) {
    if (row >= 0 && row < table_->rowCount())
        table_->item(row, COL_STATUS)->setText(text);
}

void JFJochProcessingJobsWindow::onPhase(QString phase) {
    // The "Processing images" phase is shown by onProgress; other phases (first pass, scaling, ...)
    // show their name as text over an empty bar.
    if (!running_bar_ || phase == "Processing images")
        return;
    running_bar_->setRange(0, 1);
    running_bar_->setValue(0);
    running_bar_->setFormat(phase);
}

void JFJochProcessingJobsWindow::onProgress(quint64 done, quint64 total) {
    if (!running_bar_)
        return;
    running_bar_->setRange(0, static_cast<int>(total));
    running_bar_->setValue(static_cast<int>(done));
    running_bar_->setFormat("%v / %m");

    // Processing rate and ETA in the status bar.
    if (job_timer_.isValid() && done > 0) {
        const double secs = job_timer_.elapsed() / 1000.0;
        if (secs > 0.0) {
            const double hz = done / secs;
            const double remaining = hz > 0.0 ? (total - done) / hz : 0.0;
            emit writeStatusBar(QStringLiteral("Processing %1 Hz — ~%2 s remaining")
                                    .arg(hz, 0, 'f', 1).arg(qRound(remaining)));
        }
    }
}

void JFJochProcessingJobsWindow::onFinished(ProcessResult result) {
    emit liveDataset(nullptr);   // the finished run takes over from the live overlay
    const int row = running_row_;
    running_row_ = -1;
    if (row >= 0)
        table_->removeCellWidget(row, COL_STATUS);   // deletes running_bar_
    running_bar_ = nullptr;
    if (row < 0 || row >= static_cast<int>(jobs_.size()))
        return;

    setStatus(row, result.cancelled ? "cancelled" : "done");
    if (result.indexing_rate.has_value())
        table_->item(row, COL_INDEX)->setText(QStringLiteral("%1%").arg(result.indexing_rate.value() * 100.0, 0, 'f', 0));
    if (result.consensus_cell.has_value()) {
        const auto &c = result.consensus_cell.value();
        table_->item(row, COL_CELL)->setText(
            QStringLiteral("%1 %2 %3  %4 %5 %6")
                .arg(c.a, 0, 'f', 1).arg(c.b, 0, 'f', 1).arg(c.c, 0, 'f', 1)
                .arg(c.alpha, 0, 'f', 1).arg(c.beta, 0, 'f', 1).arg(c.gamma, 0, 'f', 1));
    }

    if (!result.cancelled && result.written_master_path.has_value() && !jobs_[row].snapshot_path.isEmpty()) {
        jobs_[row].has_result = true;
        emit registerSnapshot(jobs_[row].id, jobs_[row].label, jobs_[row].snapshot_path);   // also activates it
    }

    // Capture merge statistics and surface the analysis window (auto-open once; recall later via the
    // row's graph icon).
    if (!result.cancelled && result.has_merge_statistics) {
        jobs_[row].has_merge_stats = true;
        jobs_[row].merge_stats = result.merge_statistics;
        jobs_[row].isa = result.error_model_isa;
        jobs_[row].merge_has_reference = result.has_reference;
        jobs_[row].twinning = result.twinning;
        jobs_[row].space_group_number = result.space_group_number;
        jobs_[row].space_group_search = result.space_group_search;
        if (jobs_[row].graph_btn)
            jobs_[row].graph_btn->setEnabled(true);
        showStats(jobs_[row].id);
    }

    emit writeStatusBar(result.cancelled ? "Processing cancelled" : "Processing finished");
}

void JFJochProcessingJobsWindow::onFailed(QString error) {
    emit liveDataset(nullptr);   // clear the live overlay
    const int row = running_row_;
    running_row_ = -1;
    if (row >= 0)
        table_->removeCellWidget(row, COL_STATUS);   // deletes running_bar_
    running_bar_ = nullptr;
    setStatus(row, "failed");
    QMessageBox::warning(this, "Processing failed", error);
}