Viewer: a newly opened file starts with "Known unit cell" unticked

As a bare rugnux forgets the crystal an input file stores (ClearStoredCrystal), the settings panel
now shows the file's cell and space group but does not use them until the user ticks "Known unit
cell". Before, a file carrying a cell was indexed and merged with it, like rugnux -C/-S.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

rugnux/RugnuxDefaults.h

@@ -45,7 +45,8 @@ void ApplyRugnuxExperimentDefaults(DiffractionExperiment &experiment);
 // search start de novo. A stored cell otherwise resolves the indexing algorithm to ffbidx and drives
 // it to that lattice, and a stored space group skips the search outright. The CLI calls this and then
 // applies -C / -S (or a reference MTZ) on top; the viewer instead takes the crystal straight from its
-// settings panel, which clears both fields when "Unit cell known" is unticked.
+// settings panel, which clears both fields when "Unit cell known" is unticked - as it is when a file is
+// opened.
 void ClearStoredCrystal(DiffractionExperiment &experiment);
 
 // Scaling/merging defaults for the workflow. Several differ between rotation and stills because the

viewer/JFJochViewerWindow.cpp

@@ -627,6 +627,8 @@ JFJochViewerWindow::JFJochViewerWindow(QWidget *parent, bool dbus, const QString
             reading_worker, &JFJochImageReadingWorker::FindCenter);
     connect(this, &JFJochViewerWindow::datasetReady,
             settingsPanel, &JFJochViewerSettingsDock::datasetLoaded);
+    connect(reading_worker, &JFJochImageReadingWorker::fileOpened,
+            settingsPanel, &JFJochViewerSettingsDock::fileOpened);
     connect(this, &JFJochViewerWindow::imageReady,
             settingsPanel, &JFJochViewerSettingsDock::loadImage);
     connect(settingsPanel, &JFJochViewerSettingsDock::ringsFromCalibration,

viewer/widgets/JFJochViewerSettingsDock.cpp

@@ -1022,6 +1022,10 @@ void JFJochViewerSettingsDock::datasetLoaded(std::shared_ptr<const JFJochReaderD
     ApplyProcessingMode();   // the mode just read back decides rotation vs stills
 }
 
+void JFJochViewerSettingsDock::fileOpened() {
+    cellKnown_->setChecked(false);   // a change emits the experiment without the crystal
+}
+
 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

viewer/widgets/JFJochViewerSettingsDock.h

@@ -42,6 +42,9 @@ public:
 
 public slots:
     void datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset);
+    // A new file: the crystal it stores is shown but not used until "Known unit cell" is ticked, as a
+    // bare `rugnux` forgets it (ClearStoredCrystal).
+    void fileOpened();
     void loadImage(std::shared_ptr<const JFJochReaderImage> image);
     void referenceLoaded(ReferenceMtzInfo info);   // worker reports a (un)loaded reference MTZ
     // Dataset re-processing reads a stored HDF5 file, so it is unavailable on a live HTTP stream:

viewer/windows/JFJochProcessingJobsWindow.cpp

@@ -432,10 +432,10 @@ void JFJochProcessingJobsWindow::newJob(ProcessMode mode, CalibrationSelection c
     //
     // The cell and space group come from the settings panel and nowhere else: with "Unit cell known"
     // ticked they are indexed and merged with, unticked the panel clears both and the run determines
-    // them from the data (-C / -S versus bare `rugnux`). The panel is filled from the file when one is
-    // opened, so what a run will use is always the crystal shown on screen - including after a finished
-    // job's _process.h5 becomes the active snapshot, where a run that ended in P1 shows P1 and can be
-    // cleared, rather than silently pinning every later run to it.
+    // them from the data (-C / -S versus bare `rugnux`). A newly opened file starts unticked - its stored
+    // crystal is shown but not used, as `rugnux` forgets it - so what a run uses is always the crystal
+    // shown on screen. A finished job's _process.h5 becoming the active snapshot does tick it with the
+    // run's crystal (a run that ended in P1 shows P1), which can be cleared before the next run.
     DiffractionExperiment experiment = inputs.experiment;
     const auto polarization = experiment.GetPolarizationFactor();
     ApplyRugnuxExperimentDefaults(experiment);