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Jungfraujoch/viewer/JFJochViewerWindow.cpp
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leonarski_fandClaude Opus 5 a29c36600f Beam-stop shadow detection, and a low-resolution limit for scaling 
rugnux finds the beam stop and its holder in a projection of 60 images and
marks them in the pixel mask as bit 9 (--detect-beam-stop[=N|off], on by
default). Reflections behind the stop are attenuated but not flagged, so they
integrate low with a plausible sigma and nothing downstream catches them: the
signal-box gate requires 100% valid pixels and shadow pixels are valid, the
background clip is high-side only, and the |zeta| cut applies only to the
space-group search merge.

The detection compares each pixel's background against the typical background
at the same radius on two channels. An azimuthal one (the ring median) finds
the holder arm, which is a minority of its ring; a radial one (the background
just outside) finds the disk, which the ring median cannot see because inside a
fully blocked ring the median is the shadow itself. Pixels are pooled over a
5x5 box and tested only where the background has actually been counted, so
low-background data no longer masks the whole detector. Recorded reflections
are carved back out - a beam stop cannot block a reflection that was measured.

Bit 9 belongs to the run that found it, not to the dataset: it is cleared when
a run starts, so a mask read back from a file that carries one starts clear.
The user mask (bit 8) is left alone.

Scaling and merging gain a low-resolution limit, default 50 A
(--scaling-low-resolution <num>, 0 removes it), applied per observation before
scaling so it also protects the per-frame scale fit and the space-group search.
50 A is the value XDS configurations use; rugnux_vs_xds.py now matches both of
XDS's resolution limits instead of only the high one, so the lowest shell is
the same shell in the two programs.

The viewer draws the detected shadow in coral with a "Show beam stop" switch in
the side panel, exposes the low-resolution limit in the settings dock, and
offers detection in its processing jobs. Adding an image marker meant giving
the reader a MIN_REAL_PXL_VALUE, because several places classify a pixel by
range rather than by equality and would otherwise read the new marker as a very
negative intensity.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-08-09 01:05:31 +02:00

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// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "JFJochViewerWindow.h"
#include <QThread>
#include <QDockWidget>
#include <QKeyEvent>
#include <QGuiApplication>
#include <QScreen>
#include <QScrollArea>
#include <QSettings>
#include <QCloseEvent>
#include <QRandomGenerator>
#include <QLabel>
#include <QPainter>
#include <QPushButton>
#include "JFJochImageReadingWorker.h"
#include "image_viewer/JFJochDiffractionImage.h"
#include "JFJochViewerSidePanel.h"
#include "widgets/JFJochViewerSettingsDock.h"
#include "widgets/JFJochViewerImageStrip.h"
#include "JFJochViewerStatusBar.h"
#include "../common/CUDAWrapper.h"
#include "windows/JFJochViewerImageListWindow.h"
#include "windows/JFJochViewerMetadataWindow.h"
#ifdef JFJOCH_VIEWER_DBUS
#include "dbus/JFJochViewerAdaptor.h"
#endif
#include "windows/JFJochProcessingJobsWindow.h"
#include "windows/JFJochViewerSpotListWindow.h"
#include "windows/JFJochViewerReflectionListWindow.h"
#include "windows/JFJochCalibrationWindow.h"
#include "windows/JFJochViewerReciprocalSpaceWindow.h"
#include "toolbar/JFJochViewerToolbarDisplay.h"
#include "toolbar/JFJochViewerToolbarImage.h"
#include "windows/JFJoch2DAzintImageWindow.h"
#include "windows/JFJochMagnifierWindow.h"
#include "image_viewer/JFJochImage.h"
#include "image_viewer/JFJochSimpleImage.h"
#include <QMessageBox>
// Dock-layout version for saveState/restoreState: bump whenever the dock set / structure changes so a
// stale saved layout (which can restore a dock as a broken, non-responsive floating window) is rejected
// and the default layout applies instead.
static constexpr int kLayoutVersion = 2;
JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString &file) : QMainWindow(parent) {
menuBar = new JFJochViewerMenu(this);
setMenuBar(menuBar);
// PSI logo in the menu-bar corner. There are four interchangeable dot designs; pick one at
// random each launch, for fun.
{
const int n = QRandomGenerator::global()->bounded(1, 5); // 1..4
QPixmap logoPixmap(QStringLiteral(":/psi_%1.png").arg(n, 2, 10, QLatin1Char('0')));
auto *logo = new QLabel(this);
logo->setPixmap(logoPixmap.scaledToHeight(22, Qt::SmoothTransformation));
logo->setContentsMargins(6, 0, 8, 0);
menuBar->setCornerWidget(logo, Qt::TopRightCorner);
}
setFocusPolicy(Qt::StrongFocus);
auto toolBarImage = new JFJochViewerToolbarImage(this);
toolBarImage->setObjectName("toolBarImage"); // objectName required for saveState/restoreState
addToolBar(Qt::TopToolBarArea, toolBarImage);
addToolBarBreak(Qt::TopToolBarArea);
toolBarDisplay = new JFJochViewerToolbarDisplay(this);
toolBarDisplay->setObjectName("toolBarDisplay");
addToolBar(Qt::TopToolBarArea, toolBarDisplay);
statusbar = new JFJochViewerStatusBar(this);
setStatusBar(statusbar);
setDockOptions(dockOptions() & ~QMainWindow::DockOption::AllowTabbedDocks);
setWindowTitle("Jungfraujoch image viewer");
// Start large on a big display but fit within a laptop screen.
const QRect avail = QGuiApplication::primaryScreen()->availableGeometry();
resize(qMin(1200, avail.width() - 100), qMin(1100, avail.height() - 100));
SpotFindingSettings spot_finding_settings = DiffractionExperiment::DefaultDataProcessingSettings();
// The interactive viewer is an offline tool looking at one dataset at a time, so it starts from the
// self-calibrating settings rather than numbers the user would have to tune: the per-ring adaptive
// threshold, min-pix chosen per image (std::nullopt), and detection out to the detector edge
// (high_resolution_limit unset). All three are switchable in the settings dock.
spot_finding_settings.adaptive_threshold = true;
spot_finding_settings.min_pix_per_spot = std::nullopt;
spot_finding_settings.indexing = true;
IndexingSettings indexing_settings;
indexing_settings.IndexingThreads(1);
indexing_settings.Algorithm(IndexingAlgorithmEnum::Auto);
if (get_gpu_count() == 0) {
indexing_settings.Algorithm(IndexingAlgorithmEnum::FFTW);
indexing_settings.FFT_NumVectors(8 * 1024);
}
indexing_settings.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
DiffractionExperiment experiment;
experiment.ImportIndexingSettings(indexing_settings);
experiment.DetectIceRings(true);
// Central area: the diffraction image. Everything else (inspector, plots, processing) is a
// dock, so the layout can be rearranged, saved, and switched between perspectives.
auto viewer = new JFJochDiffractionImage(this);
viewer->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding);
setCentralWidget(viewer);
auto side_panel = new JFJochViewerSidePanel(this);
auto side_panel_scroll = new QScrollArea(this);
side_panel_scroll->setWidget(side_panel);
side_panel_scroll->setWidgetResizable(true);
side_panel_scroll->setHorizontalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
side_panel_scroll->setVerticalScrollBarPolicy(Qt::ScrollBarAsNeeded);
side_panel_scroll->setMinimumWidth(450);
side_panel_scroll->setMaximumWidth(600);
inspectorDock = new QDockWidget("Inspector", this);
inspectorDock->setObjectName("inspectorDock");
inspectorDock->setAllowedAreas(Qt::LeftDockWidgetArea | Qt::RightDockWidgetArea);
inspectorDock->setWidget(side_panel_scroll);
addDockWidget(Qt::RightDockWidgetArea, inspectorDock);
menuBar->AddDockEntry(inspectorDock, "Inspector");
reading_worker = new JFJochImageReadingWorker(spot_finding_settings, experiment);
reading_thread = new QThread(this);
reading_worker->moveToThread(reading_thread);
reading_thread->start();
auto tableWindow = new JFJochViewerImageListWindow(this);
auto metadataWindow = new JFJochViewerMetadataWindow(this);
auto spotWindow = new JFJochViewerSpotListWindow(this);
auto reflectionWindow = new JFJochViewerReflectionListWindow(this);
auto calibrationWindow = new JFJochCalibrationWindow(this);
auto reciprocalWindow = new JFJochViewerReciprocalSpaceWindow(this);
auto azintImageWindow = new JFJoch2DAzintImageWindow(this);
auto magnifierWindow = new JFJochMagnifierWindow(this);
processingJobsWindow = new JFJochProcessingJobsWindow(reading_worker, this);
// The two hero actions (re-analyse the current image / the whole dataset) live at the top of the
// settings panel now — see the JFJochViewerSettingsDock wiring below.
menuBar->AddWindowEntry(tableWindow, "Image list");
menuBar->AddWindowEntry(spotWindow, "Spot list");
menuBar->AddWindowEntry(reflectionWindow, "Reflection list");
menuBar->AddWindowEntry(metadataWindow, "Image metadata");
menuBar->AddWindowEntry(calibrationWindow, "Calibration image viewer");
menuBar->AddWindowEntry(reciprocalWindow, "Reciprocal space viewer");
menuBar->AddWindowEntry(azintImageWindow, "Azimuthal integration 2D image");
menuBar->AddWindowEntry(magnifierWindow, "Magnifier");
// processingJobsWindow is docked (bottom, next to the plots), not a standalone window - see below.
#ifdef JFJOCH_VIEWER_DBUS
if (dbus) {
// Create adaptor attached to this window
new JFJochViewerAdaptor(this);
QDBusConnection connection = QDBusConnection::sessionBus();
if (!connection.registerService("ch.psi.jfjoch_viewer")) {
qWarning("Failed to register D-Bus service: %s", qPrintable(connection.lastError().message()));
} else {
if (!connection.registerObject("/", this, QDBusConnection::ExportAdaptors)) {
qFatal("Failed to register D-Bus object: %s", qPrintable(connection.lastError().message()));
}
}
}
#else
(void) dbus;
#endif
connect(this, &JFJochViewerWindow::LoadFileRequest,
reading_worker, &JFJochImageReadingWorker::LoadFile);
connect(this, &JFJochViewerWindow::LoadImageRequest,
reading_worker, &JFJochImageReadingWorker::LoadImage);
connect(menuBar, &JFJochViewerMenu::fileOpenSelected,
reading_worker, &JFJochImageReadingWorker::LoadFile);
connect(menuBar, &JFJochViewerMenu::fileCloseSelected,
reading_worker, &JFJochImageReadingWorker::CloseFile);
// The worker runs in its own thread; its imageLoaded crosses the thread boundary exactly once,
// into OnImageReady, which re-emits imageReady to every GUI consumer synchronously (same thread)
// and then acks the worker (imageConsumed). Routing all consumers through one window signal makes
// the ack land after they have all run, and lets the worker cap how many frames are in flight.
connect(reading_worker, &JFJochImageReadingWorker::imageLoaded,
this, &JFJochViewerWindow::OnImageReady);
connect(this, &JFJochViewerWindow::imageConsumed,
reading_worker, &JFJochImageReadingWorker::ImageConsumed);
// Dataset stream routed the same way, so it gets the same backpressure: the worker's datasetLoaded
// crosses the thread boundary once into OnDatasetReady, which re-emits datasetReady to every GUI
// consumer synchronously and then acks the worker (datasetConsumed).
connect(reading_worker, &JFJochImageReadingWorker::datasetLoaded,
this, &JFJochViewerWindow::OnDatasetReady);
connect(this, &JFJochViewerWindow::datasetConsumed,
reading_worker, &JFJochImageReadingWorker::DatasetConsumed);
connect(this, &JFJochViewerWindow::imageReady,
viewer, &JFJochDiffractionImage::loadImage);
connect(this, &JFJochViewerWindow::imageReady,
side_panel, &JFJochViewerSidePanel::loadImage);
connect(reading_worker, &JFJochImageReadingWorker::imageStatsUpdated,
side_panel, &JFJochViewerSidePanel::loadImage);
connect(reading_worker, &JFJochImageReadingWorker::imageNumberChanged, toolBarImage,
&JFJochViewerToolbarImage::setImageNumber);
connect(toolBarImage, &JFJochViewerToolbarImage::loadImage, reading_worker, &JFJochImageReadingWorker::LoadImage);
connect(toolBarDisplay, &JFJochViewerToolbarDisplay::setForeground, viewer,
&JFJochDiffractionImage::changeForeground);
connect(viewer, &JFJochDiffractionImage::autoForegroundChanged,
toolBarDisplay, &JFJochViewerToolbarDisplay::updateAutoForeground);
connect(toolBarDisplay, &JFJochViewerToolbarDisplay::setAutoForeground, viewer,
&JFJochDiffractionImage::setAutoForeground);
connect(toolBarDisplay, &JFJochViewerToolbarDisplay::setHDRMode, viewer,
&JFJochDiffractionImage::setHDRMode);
connect(toolBarDisplay, &JFJochViewerToolbarDisplay::colorMapChanged, viewer,
&JFJochDiffractionImage::setColorMap);
connect(toolBarDisplay, &JFJochViewerToolbarDisplay::colorMapChanged, azintImageWindow,
&JFJoch2DAzintImageWindow::setColorMap);
connect(this, &JFJochViewerWindow::imageReady,
azintImageWindow, &JFJoch2DAzintImageWindow::imageLoaded);
connect(viewer, &JFJochDiffractionImage::foregroundChanged,
toolBarDisplay, &JFJochViewerToolbarDisplay::updateForeground);
connect(side_panel, &JFJochViewerSidePanel::roisChanged,
reading_worker, &JFJochImageReadingWorker::SetROIDefinition);
connect(side_panel, &JFJochViewerSidePanel::selectedROIChanged,
viewer, &JFJochDiffractionImage::setSelectedROI);
connect(viewer, &JFJochDiffractionImage::roiGeometryEdited,
reading_worker, &JFJochImageReadingWorker::SetROIDefinition);
connect(viewer, &JFJochDiffractionImage::roiSelected,
side_panel, &JFJochViewerSidePanel::selectROIInList);
connect(side_panel, &JFJochViewerSidePanel::downloadROIs,
reading_worker, &JFJochImageReadingWorker::DownloadROIsFromServer);
connect(side_panel, &JFJochViewerSidePanel::uploadROIs,
reading_worker, &JFJochImageReadingWorker::UploadROIsToServer);
connect(side_panel, &JFJochViewerSidePanel::maskFromROI,
reading_worker, &JFJochImageReadingWorker::MaskFromSelectedROI);
connect(menuBar, &JFJochViewerMenu::clearUserMaskSelected,
reading_worker, &JFJochImageReadingWorker::ClearUserMask);
connect(menuBar, &JFJochViewerMenu::saveUserMaskTiffSelected,
reading_worker, &JFJochImageReadingWorker::SaveUserMaskTIFF);
connect(menuBar, &JFJochViewerMenu::loadUserMaskTiffSelected,
reading_worker, &JFJochImageReadingWorker::LoadUserMaskTIFF);
connect(menuBar, &JFJochViewerMenu::uploadUserMaskSelected,
reading_worker, &JFJochImageReadingWorker::UploadUserMask);
connect(this, &JFJochViewerWindow::datasetReady,
tableWindow, &JFJochViewerImageListWindow::datasetLoaded);
connect(this, &JFJochViewerWindow::datasetReady,
spotWindow, &JFJochViewerSpotListWindow::datasetLoaded);
connect(this, &JFJochViewerWindow::datasetReady,
metadataWindow, &JFJochViewerMetadataWindow::datasetLoaded);
connect(this, &JFJochViewerWindow::imageReady,
tableWindow, &JFJochViewerImageListWindow::imageLoaded);
connect(this, &JFJochViewerWindow::imageReady,
spotWindow, &JFJochViewerSpotListWindow::imageLoaded);
connect(tableWindow, &JFJochViewerImageListWindow::imageSelected,
reading_worker, &JFJochImageReadingWorker::LoadImage);
connect(reading_worker, &JFJochImageReadingWorker::autoloadChanged,
toolBarImage, &JFJochViewerToolbarImage::setAutoloadMode);
connect(toolBarImage, &JFJochViewerToolbarImage::autoLoadButtonPressed,
reading_worker, &JFJochImageReadingWorker::setAutoLoadMode);
connect(toolBarImage, &JFJochViewerToolbarImage::imageJumpChanged,
reading_worker, &JFJochImageReadingWorker::setAutoLoadJump);
// HTTP-sync button: reflect the live connection, and open the connect dialog when clicked
// while no live source is attached (i.e. a plain file is open).
connect(reading_worker, &JFJochImageReadingWorker::httpConnectionChanged,
toolBarImage, &JFJochViewerToolbarImage::setHttpConnection);
connect(toolBarImage, &JFJochViewerToolbarImage::requestHttpConnect,
menuBar, &JFJochViewerMenu::openHttpSelected);
connect(toolBarImage, &JFJochViewerToolbarImage::requestOpenFile,
menuBar, &JFJochViewerMenu::openSelected);
connect(side_panel, &JFJochViewerSidePanel::analyze,
reading_worker, &JFJochImageReadingWorker::Analyze);
connect(side_panel, &JFJochViewerSidePanel::findBeamCenter,
reading_worker, &JFJochImageReadingWorker::FindCenter);
connect(this, &JFJochViewerWindow::datasetReady,
reflectionWindow, &JFJochViewerReflectionListWindow::datasetLoaded);
connect(this, &JFJochViewerWindow::imageReady,
reflectionWindow, &JFJochViewerReflectionListWindow::imageLoaded);
connect(reflectionWindow, &JFJochHelperWindow::zoom, viewer, &JFJochDiffractionImage::centerOnSpot);
connect(spotWindow, &JFJochHelperWindow::zoom, viewer, &JFJochDiffractionImage::centerOnSpot);
connect(side_panel, &JFJochViewerSidePanel::showSpots,
viewer, &JFJochDiffractionImage::showSpots);
connect(side_panel, &JFJochViewerSidePanel::showPredictions,
viewer, &JFJochDiffractionImage::showPredictions);
connect(side_panel, &JFJochViewerSidePanel::showROILabels,
viewer, &JFJochDiffractionImage::showROILabels);
connect(side_panel, &JFJochViewerSidePanel::showROIFill,
viewer, &JFJochDiffractionImage::showROIFill);
connect(side_panel, &JFJochViewerSidePanel::setFeatureColor,
viewer, &JFJochDiffractionImage::setFeatureColor);
connect(side_panel, &JFJochViewerSidePanel::setFeatureColor,
calibrationWindow, &JFJochCalibrationWindow::setFeatureColor);
connect(side_panel, &JFJochViewerSidePanel::setSpotColor,
viewer, &JFJochDiffractionImage::setSpotColor);
connect(side_panel, &JFJochViewerSidePanel::showHighestPixels,
viewer, &JFJochDiffractionImage::showHighestPixels);
connect(side_panel, &JFJochViewerSidePanel::showSaturatedPixels,
viewer, &JFJochDiffractionImage::showSaturation);
connect(side_panel, &JFJochViewerSidePanel::showBeamStop,
viewer, &JFJochDiffractionImage::showBeamStop);
connect(viewer, &JFJochDiffractionImage::writeStatusBar,
statusbar, &JFJochViewerStatusBar::display);
connect(side_panel, &JFJochViewerSidePanel::writeStatusBar,
statusbar, &JFJochViewerStatusBar::display);
// Detector connection / broker state / live readouts in the status bar
connect(reading_worker, &JFJochImageReadingWorker::brokerStatusUpdated,
statusbar, &JFJochViewerStatusBar::setBrokerStatus);
connect(reading_worker, &JFJochImageReadingWorker::httpConnectionChanged,
statusbar, &JFJochViewerStatusBar::setHttpConnection);
connect(reading_worker, &JFJochImageReadingWorker::autoloadChanged,
statusbar, &JFJochViewerStatusBar::setAutoloadMode);
connect(reading_worker, &JFJochImageReadingWorker::imageNumberChanged,
statusbar, &JFJochViewerStatusBar::setImageNumber);
connect(reading_worker, &JFJochImageReadingWorker::liveRateChanged,
statusbar, &JFJochViewerStatusBar::setLiveRate);
connect(metadataWindow, &JFJochViewerMetadataWindow::datasetUpdated,
reading_worker, &JFJochImageReadingWorker::UpdateDataset);
connect(reading_worker, &JFJochImageReadingWorker::setRings,
side_panel, &JFJochViewerSidePanel::SetRings);
connect(side_panel, &JFJochViewerSidePanel::resRingsSet,
viewer, &JFJochDiffractionImage::setResolutionRing);
connect(side_panel, &JFJochViewerSidePanel::ringModeSet,
viewer, &JFJochDiffractionImage::setResolutionRingMode);
connect(side_panel, &JFJochViewerSidePanel::highlightIceRings,
viewer, &JFJochDiffractionImage::highlightIceRings);
connect(calibrationWindow, &JFJochCalibrationWindow::loadCalibration,
reading_worker, &JFJochImageReadingWorker::LoadCalibration);
connect(this, &JFJochViewerWindow::datasetReady,
calibrationWindow, &JFJochCalibrationWindow::datasetLoaded);
connect(reading_worker, &JFJochImageReadingWorker::simpleImageLoaded,
calibrationWindow, &JFJochCalibrationWindow::calibrationLoaded);
connect(this, &JFJochViewerWindow::datasetReady,
reciprocalWindow, &JFJochViewerReciprocalSpaceWindow::datasetLoaded);
connect(this, &JFJochViewerWindow::imageReady,
reciprocalWindow, &JFJochViewerReciprocalSpaceWindow::imageLoaded);
connect(reciprocalWindow, &JFJochViewerReciprocalSpaceWindow::loadSpotsRequest,
reading_worker, &JFJochImageReadingWorker::LoadSpots);
connect(reading_worker, &JFJochImageReadingWorker::spotsLoaded,
reciprocalWindow, &JFJochViewerReciprocalSpaceWindow::spotsLoaded);
connect(reciprocalWindow, &JFJochHelperWindow::zoom,
viewer, &JFJochDiffractionImage::centerOnSpot);
connect(side_panel, &JFJochViewerSidePanel::setSpotColor,
reciprocalWindow, &JFJochViewerReciprocalSpaceWindow::setSpotColor);
connect(side_panel, &JFJochViewerSidePanel::setFeatureColor,
reciprocalWindow, &JFJochViewerReciprocalSpaceWindow::setFeatureColor);
connect(azintImageWindow, &JFJoch2DAzintImageWindow::zoomOnBin,
viewer, &JFJochDiffractionImage::centerOnSpot);
// --- Magnifier ---
// The magnifier shows the frame the main view has already rendered - the same pixels with
// its own zoom and centre - so it neither converts nor colours anything itself.
connect(viewer, &JFJochImage::frameRendered, magnifierWindow, [viewer, magnifierWindow] {
magnifierWindow->setFrame(viewer->Frame());
});
// ... and the raw counts behind it, for the per-pixel labels. Stores a pointer, nothing more.
connect(this, &JFJochViewerWindow::imageReady,
magnifierWindow, &JFJochHelperWindow::imageLoaded);
connect(viewer, &JFJochImage::hoverScenePos,
magnifierWindow, &JFJochMagnifierWindow::centerAt);
// Ensure worker is deleted in its own thread when the thread stops
connect(reading_thread, &QThread::finished, reading_worker, &QObject::deleteLater);
// lastDataset and lastImage are captured in OnDatasetReady / OnImageReady, which see every
// dataset / frame before fanning them out.
connect(this, &JFJochViewerWindow::imageReady,
toolBarDisplay, &JFJochViewerToolbarDisplay::imageLoaded);
connect(reading_worker, &JFJochImageReadingWorker::fileLoadError,
this, &JFJochViewerWindow::OnFileLoadError);
connect(reading_worker, &JFJochImageReadingWorker::fileLoadRetryStatus,
this, &JFJochViewerWindow::OnFileLoadRetryStatus);
connect(menuBar, &JFJochViewerMenu::openDatasetInfo, this, &JFJochViewerWindow::NewDatasetInfo);
NewDatasetInfo();
connect(this, &JFJochViewerWindow::adjustForegroundButton,
viewer, &JFJochDiffractionImage::adjustForeground);
connect(this, &JFJochViewerWindow::setAutoForeground,
viewer, &JFJochDiffractionImage::setAutoForeground);
// Processing jobs: run rugnux locally / copy a cluster command line, and surface
// finished runs as switchable dataset snapshots.
connect(processingJobsWindow, &JFJochProcessingJobsWindow::registerSnapshot,
reading_worker, &JFJochImageReadingWorker::RegisterProcessingSnapshot);
connect(processingJobsWindow, &JFJochProcessingJobsWindow::activateSnapshot,
reading_worker, &JFJochImageReadingWorker::SetActiveSnapshot);
connect(processingJobsWindow, &JFJochProcessingJobsWindow::writeStatusBar,
statusbar, &JFJochViewerStatusBar::display);
connect(processingJobsWindow, &JFJochProcessingJobsWindow::renameRun,
reading_worker, &JFJochImageReadingWorker::RenameRun);
connect(processingJobsWindow, &JFJochProcessingJobsWindow::removeRun,
reading_worker, &JFJochImageReadingWorker::RemoveRun);
connect(reading_worker, &JFJochImageReadingWorker::httpConnectionChanged,
processingJobsWindow, &JFJochProcessingJobsWindow::onHttpConnectionChanged);
connect(reading_worker, &JFJochImageReadingWorker::fileOpened,
processingJobsWindow, &JFJochProcessingJobsWindow::clearJobs);
connect(reading_worker, &JFJochImageReadingWorker::snapshotsChanged, processingJobsWindow,
[pw = processingJobsWindow](QStringList, QString active) { pw->setActiveRun(active); });
connect(reading_worker, &JFJochImageReadingWorker::runsChanged, this,
[this](QVector<RunData> runs, QString active) {
lastRuns = std::move(runs);
lastActiveRunId = std::move(active);
});
// Inline settings dock: the surgical MX/AzInt subset, always visible (left), wired straight
// into the running analysis so edits re-run on the current image / dataset.
auto *settingsPanel = new JFJochViewerSettingsDock(spot_finding_settings, indexing_settings,
experiment.GetAzimuthalIntegrationSettings(),
experiment.GetBraggIntegrationSettings(),
experiment.GetScalingSettings(), this);
// The panel's natural minimum (a long reference-consistency warning, the geometry rows, …) would
// otherwise pin the dock wide and stop it folding back; setMinimumWidth(0) lets the scroll area's
// own minimum (330) govern the fold. The horizontal scrollbar is AlwaysOff (like the inspector
// dock): with widgetResizable, both-axes ScrollBarAsNeeded oscillates (a vertical bar narrows the
// viewport -> a horizontal bar appears -> shortens it -> vertical fits -> ...), which pegs the CPU
// and freezes the panel when floated.
settingsPanel->setMinimumWidth(0);
auto *settingsScroll = new QScrollArea(this);
settingsScroll->setWidget(settingsPanel);
settingsScroll->setWidgetResizable(true);
settingsScroll->setHorizontalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
settingsScroll->setVerticalScrollBarPolicy(Qt::ScrollBarAsNeeded);
settingsScroll->setMinimumWidth(330);
settingsScroll->setMaximumWidth(480);
settingsDock = new QDockWidget("Settings", this);
settingsDock->setObjectName("settingsDock");
settingsDock->setAllowedAreas(Qt::LeftDockWidgetArea | Qt::RightDockWidgetArea);
settingsDock->setWidget(settingsScroll); // scrollable: don't force the window taller than the screen
addDockWidget(Qt::LeftDockWidgetArea, settingsDock);
menuBar->AddDockEntry(settingsDock, "Settings");
connect(settingsPanel, &JFJochViewerSettingsDock::spotFindingChanged,
reading_worker, &JFJochImageReadingWorker::UpdateSpotFindingSettings);
connect(settingsPanel, &JFJochViewerSettingsDock::azintChanged,
reading_worker, &JFJochImageReadingWorker::UpdateAzintSettings);
connect(settingsPanel, &JFJochViewerSettingsDock::braggChanged,
reading_worker, &JFJochImageReadingWorker::UpdateBraggIntegrationSettings);
connect(settingsPanel, &JFJochViewerSettingsDock::scalingChanged,
reading_worker, &JFJochImageReadingWorker::UpdateScalingSettings);
// The two analysis actions now live on top of the panel.
connect(settingsPanel, &JFJochViewerSettingsDock::reanalyzeImage,
reading_worker, &JFJochImageReadingWorker::ReanalyzeImages);
connect(settingsPanel, &JFJochViewerSettingsDock::analyzeDataset,
processingJobsWindow, &JFJochProcessingJobsWindow::newJob);
// Grey out "Analyze dataset" on a live HTTP source (re-processing needs a stored file).
connect(reading_worker, &JFJochImageReadingWorker::httpConnectionChanged,
settingsPanel, &JFJochViewerSettingsDock::setHttpConnection);
connect(settingsPanel, &JFJochViewerSettingsDock::experimentChanged,
reading_worker, &JFJochImageReadingWorker::UpdateDataset);
connect(settingsPanel, &JFJochViewerSettingsDock::findBeamCenter,
reading_worker, &JFJochImageReadingWorker::FindCenter);
connect(this, &JFJochViewerWindow::datasetReady,
settingsPanel, &JFJochViewerSettingsDock::datasetLoaded);
connect(this, &JFJochViewerWindow::imageReady,
settingsPanel, &JFJochViewerSettingsDock::loadImage);
connect(settingsPanel, &JFJochViewerSettingsDock::ringsFromCalibration,
side_panel, &JFJochViewerSidePanel::SetRings);
connect(settingsPanel, &JFJochViewerSettingsDock::referenceSelected,
reading_worker, &JFJochImageReadingWorker::SetReferenceMtz);
connect(reading_worker, &JFJochImageReadingWorker::referenceMtzChanged,
settingsPanel, &JFJochViewerSettingsDock::referenceLoaded);
// Processing panel: hidden by default and narrower; it reveals itself (to the right of the
// plots) only when a reprocessing job starts.
processingDock = new QDockWidget("Processing", this);
processingDock->setObjectName("processingDock");
// Allow any area so dragging it out (floating) and re-docking behave; the table's natural width
// (its columns) must not pin the dock wide, so let it fold like the settings dock.
processingDock->setAllowedAreas(Qt::AllDockWidgetAreas);
processingDock->setFeatures(
QDockWidget::DockWidgetMovable | QDockWidget::DockWidgetFloatable | QDockWidget::DockWidgetClosable);
processingJobsWindow->setMinimumWidth(0);
processingDock->setWidget(processingJobsWindow);
addDockWidget(Qt::BottomDockWidgetArea, processingDock);
if (lastDatasetInfoDock) {
splitDockWidget(lastDatasetInfoDock, processingDock, Qt::Horizontal);
resizeDocks({lastDatasetInfoDock, processingDock}, {900, 280}, Qt::Horizontal);
}
processingDock->hide();
menuBar->AddDockEntry(processingDock, "Processing");
connect(processingJobsWindow, &JFJochProcessingJobsWindow::jobStarted, this, [this] {
processingDock->show();
processingDock->raise();
});
// Image strip / hit feed: thumbnails of representative images, rendered off-thread; click opens.
// Stacked below the plots — both want vertical room, and the strip needs less of it.
auto *imageStrip = new JFJochViewerImageStrip(this);
imageStripDock = new QDockWidget("Image strip", this);
imageStripDock->setObjectName("imageStripDock");
imageStripDock->setWidget(imageStrip);
addDockWidget(Qt::BottomDockWidgetArea, imageStripDock);
if (lastDatasetInfoDock) {
splitDockWidget(lastDatasetInfoDock, imageStripDock, Qt::Vertical);
resizeDocks({lastDatasetInfoDock, imageStripDock}, {260, 140}, Qt::Vertical);
}
menuBar->AddDockEntry(imageStripDock, "Image strip");
connect(this, &JFJochViewerWindow::datasetReady,
imageStrip, &JFJochViewerImageStrip::datasetLoaded);
connect(reading_worker, &JFJochImageReadingWorker::fileOpened,
imageStrip, &JFJochViewerImageStrip::resetForNewFile);
connect(imageStrip, &JFJochViewerImageStrip::requestThumbnails,
reading_worker, &JFJochImageReadingWorker::RenderThumbnails);
connect(reading_worker, &JFJochImageReadingWorker::thumbnailReady,
imageStrip, &JFJochViewerImageStrip::thumbnailReady);
connect(imageStrip, &JFJochViewerImageStrip::imageSelected,
reading_worker, &JFJochImageReadingWorker::LoadImage);
connect(toolBarDisplay, &JFJochViewerToolbarDisplay::colorMapChanged,
reading_worker, &JFJochImageReadingWorker::SetThumbnailColorMap);
connect(side_panel, &JFJochViewerSidePanel::setFeatureColor,
reading_worker, &JFJochImageReadingWorker::SetThumbnailFeatureColor);
connect(side_panel, &JFJochViewerSidePanel::setSpotColor,
reading_worker, &JFJochImageReadingWorker::SetThumbnailSpotColor);
connect(menuBar, &JFJochViewerMenu::imageLayoutSelected, this,
[this] { ApplyPerspective(Perspective::Image); });
connect(menuBar, &JFJochViewerMenu::processingLayoutSelected, this,
[this] { ApplyPerspective(Perspective::Processing); });
connect(menuBar, &JFJochViewerMenu::resetLayoutSelected, this,
[this] { if (!defaultLayoutState.isEmpty()) restoreState(defaultLayoutState, kLayoutVersion); });
// Tear-off floating is disabled for all docks: a floated QDockWidget is unreliable across platforms
// (on WSLg it becomes an off-screen, override-redirect window that can't be focused or recovered, so
// the undocked panel goes dead). Docks stay movable between dock areas and closable, just not floated.
for (QDockWidget *dock : findChildren<QDockWidget *>())
dock->setFeatures(dock->features() & ~QDockWidget::DockWidgetFloatable);
// Remember the freshly-built layout so "Reset layout" can return to it, then restore the
// user's last-used arrangement if they have one (and if it matches the current layout version).
defaultLayoutState = saveState(kLayoutVersion);
QSettings settings("PSI", "jfjoch_viewer");
restoreGeometry(settings.value("geometry").toByteArray());
restoreState(settings.value("windowState").toByteArray(), kLayoutVersion);
if (!file.isEmpty())
LoadFile(file, 0, 1, false);
}
JFJochViewerWindow::~JFJochViewerWindow() {
if (reading_thread && reading_thread->isRunning()) {
reading_thread->quit();
reading_thread->wait();
}
}
void JFJochViewerWindow::ApplyPerspective(Perspective p) {
// Image: just the image + inspector. Processing: also settings, dataset-info plots, jobs panel.
const bool processing = (p == Perspective::Processing);
if (inspectorDock) inspectorDock->setVisible(true);
if (settingsDock) settingsDock->setVisible(processing);
if (imageStripDock) imageStripDock->setVisible(processing);
if (processingDock && !processing) processingDock->hide(); // shows only when a job starts
for (auto *d : findChildren<QDockWidget *>())
if (d->objectName().startsWith("datasetInfoDock"))
d->setVisible(processing);
}
void JFJochViewerWindow::closeEvent(QCloseEvent *event) {
// Persist the dock/toolbar arrangement and window geometry so the next launch resumes it.
QSettings settings("PSI", "jfjoch_viewer");
settings.setValue("geometry", saveGeometry());
settings.setValue("windowState", saveState(kLayoutVersion));
QMainWindow::closeEvent(event);
}
void JFJochViewerWindow::LoadFile(const QString &filename, qint64 image_number, qint64 summation, bool retry) {
emit LoadFileRequest(filename, image_number, summation, true);
}
void JFJochViewerWindow::LoadImage(qint64 image_number, qint64 summation) {
emit LoadImageRequest(image_number, summation);
}
void JFJochViewerWindow::OnImageReady(std::shared_ptr<const JFJochReaderImage> image) {
lastImage = image; // newest frame, for dataset-info docks opened later
emit imageReady(image); // fan out to every GUI consumer synchronously (same thread)
emit imageConsumed(); // ack the worker so it may fetch/produce the next frame
}
void JFJochViewerWindow::OnDatasetReady(std::shared_ptr<const JFJochReaderDataset> dataset) {
lastDataset = dataset; // newest dataset, for dataset-info docks opened later
emit datasetReady(dataset); // fan out to every GUI consumer synchronously (same thread)
emit datasetConsumed(); // ack the worker so it may produce the next dataset refresh
}
void JFJochViewerWindow::NewDatasetInfo() {
auto info = new JFJochViewerDatasetInfo(this);
info->datasetLoaded(lastDataset);
info->imageLoaded(lastImage);
info->runsChanged(lastRuns, lastActiveRunId);
auto dock = new QDockWidget(QString("Dataset info"), this);
dock->setObjectName(QStringLiteral("datasetInfoDock%1").arg(datasetInfoCounter++));
dock->setAllowedAreas(Qt::BottomDockWidgetArea);
dock->setFeatures(
QDockWidget::DockWidgetMovable | QDockWidget::DockWidgetFloatable | QDockWidget::DockWidgetClosable |
QDockWidget::DockWidgetVerticalTitleBar);
dock->setAttribute(Qt::WA_DeleteOnClose);
dock->setWidget(info);
addDockWidget(Qt::BottomDockWidgetArea, dock);
// Place additional plots beside the previous one so "+ Plot" gives a visible row of plots.
if (lastDatasetInfoDock)
splitDockWidget(lastDatasetInfoDock, dock, Qt::Horizontal);
lastDatasetInfoDock = dock;
// Wire signals like the initial dataset_info
connect(this, &JFJochViewerWindow::datasetReady,
info, &JFJochViewerDatasetInfo::datasetLoaded);
connect(this, &JFJochViewerWindow::imageReady,
info, &JFJochViewerDatasetInfo::imageLoaded);
// All runs (original + reprocessing snapshots) overlay as separate lines.
connect(reading_worker, &JFJochImageReadingWorker::runsChanged,
info, &JFJochViewerDatasetInfo::runsChanged);
// Live processing results: the in-progress run as its own overlay line.
connect(processingJobsWindow, &JFJochProcessingJobsWindow::liveDataset,
info, &JFJochViewerDatasetInfo::liveRunUpdated);
connect(info, &JFJochViewerDatasetInfo::imageSelected,
reading_worker, &JFJochImageReadingWorker::LoadImage);
connect(info, &JFJochViewerDatasetInfo::addPlot, this, &JFJochViewerWindow::NewDatasetInfo);
connect(toolBarDisplay, &JFJochViewerToolbarDisplay::colorMapChanged,
info, &JFJochViewerDatasetInfo::setColorMap);
connect(info, &JFJochViewerDatasetInfo::writeStatusBar,
statusbar, &JFJochViewerStatusBar::display);
}
void JFJochViewerWindow::keyPressEvent(QKeyEvent *event) {
if (event->key() == Qt::Key_F) {
emit adjustForegroundButton(true);
event->accept();
return;
}
if (event->key() == Qt::Key_A && ! event->isAutoRepeat()) {
emit setAutoForeground(true);
event->accept();
return;
}
QMainWindow::keyPressEvent(event);
}
void JFJochViewerWindow::keyReleaseEvent(QKeyEvent *event) {
if (event->key() == Qt::Key_F) {
emit adjustForegroundButton(false);
event->accept();
return;
}
QMainWindow::keyReleaseEvent(event);
}
void JFJochViewerWindow::OnFileLoadError(QString title, QString message) {
QMessageBox::critical(this, title, message);
}
void JFJochViewerWindow::OnFileLoadRetryStatus(bool active, QString message) {
if (active) {
if (!retryDialog) {
retryDialog = new QProgressDialog(this);
retryDialog->setWindowModality(Qt::WindowModal);
retryDialog->setRange(0, 0); // Infinite/Busy indicator
retryDialog->setCancelButton(nullptr); // Disable cancel for now
retryDialog->setMinimumDuration(0); // Show immediately
retryDialog->setWindowTitle("Loading File");
}
retryDialog->setLabelText(message);
retryDialog->show();
} else {
if (retryDialog) {
retryDialog->close();
retryDialog->deleteLater();
retryDialog = nullptr;
}
}
}
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